diff --git a/annotationPipeline/src/test/java/org/cbioportal/annotation/SpringBatchIntegrationTest.java b/annotationPipeline/src/test/java/org/cbioportal/annotation/SpringBatchIntegrationTest.java index 61e976f4..8ef57755 100644 --- a/annotationPipeline/src/test/java/org/cbioportal/annotation/SpringBatchIntegrationTest.java +++ b/annotationPipeline/src/test/java/org/cbioportal/annotation/SpringBatchIntegrationTest.java @@ -68,7 +68,7 @@ public void check_if_maf_file_still_the_same_when_annotating_with_uniprot_transc JobParameters jobParameters = new JobParametersBuilder() .addString("filename", inputFile) .addString("outputFilename", actualFile) - .addString("replace", String.valueOf(false)) + .addString("replace", String.valueOf(true)) .addString("isoformOverride", "uniprot") .addString("errorReportLocation", null) .toJobParameters(); @@ -85,7 +85,7 @@ public void check_if_maf_file_still_the_same_when_annotating_with_mskcc_transcri JobParameters jobParameters = new JobParametersBuilder() .addString("filename", inputFile) .addString("outputFilename", actualFile) - .addString("replace", String.valueOf(false)) + .addString("replace", String.valueOf(true)) .addString("isoformOverride", "mskcc") .addString("errorReportLocation", null) .toJobParameters(); @@ -192,7 +192,7 @@ public void run_vcf2maf_test_case_mskcc() throws Exception { JobParameters jobParameters = new JobParametersBuilder() .addString("filename", inputFile) .addString("outputFilename", actualFile) - .addString("replace", String.valueOf(false)) + .addString("replace", String.valueOf(true)) .addString("isoformOverride", "mskcc") .addString("errorReportLocation", null) .toJobParameters(); @@ -214,7 +214,7 @@ public void run_vcf2maf_test_case_uniprot() throws Exception { JobParameters jobParameters = new JobParametersBuilder() .addString("filename", inputFile) .addString("outputFilename", actualFile) - .addString("replace", String.valueOf(false)) + .addString("replace", String.valueOf(true)) .addString("isoformOverride", "uniprot") .addString("errorReportLocation", null) .toJobParameters(); @@ -248,7 +248,7 @@ public void check_if_nucleotide_context_provides_Ref_Tri_and_Var_Tri_columns() t JobParameters jobParameters = new JobParametersBuilder() .addString("filename", inputFile) .addString("outputFilename", actualFile) - .addString("replace", String.valueOf(false)) + .addString("replace", String.valueOf(true)) .addString("isoformOverride", "uniprot") .addString("errorReportLocation", null) .toJobParameters(); diff --git a/annotationPipeline/src/test/resources/expected/corner_cases.mskcc.txt b/annotationPipeline/src/test/resources/expected/corner_cases.mskcc.txt index 70891097..c3be1839 100644 --- a/annotationPipeline/src/test/resources/expected/corner_cases.mskcc.txt +++ b/annotationPipeline/src/test/resources/expected/corner_cases.mskcc.txt @@ -1,5 +1,5 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.mskcc.txt b/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.mskcc.txt index fe245c40..890ed668 100644 --- a/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.mskcc.txt +++ b/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.mskcc.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS -KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 Start position changes from 17796382 to 17796383 is attributed to the presence of common bases A. Reference allele changes from AC to C is attributed to the presence of common bases A. Variant allele changes from AAC to AC is attributed to the presence of common bases A. SUCCESS +KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 Start position changes from 17796381 to 17796382 is attributed to the presence of common bases A. Reference allele changes from AAC to AC is attributed to the presence of common bases A. Variant allele changes from AGT to GT is attributed to the presence of common bases A. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.uniprot.txt b/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.uniprot.txt index 7b6ec286..ca9c576c 100644 --- a/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS -KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 Start position changes from 17796382 to 17796383 is attributed to the presence of common bases A. Reference allele changes from AC to C is attributed to the presence of common bases A. Variant allele changes from AAC to AC is attributed to the presence of common bases A. SUCCESS +KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 Start position changes from 17796381 to 17796382 is attributed to the presence of common bases A. Reference allele changes from AAC to AC is attributed to the presence of common bases A. Variant allele changes from AGT to GT is attributed to the presence of common bases A. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/corner_cases.uniprot.txt b/annotationPipeline/src/test/resources/expected/corner_cases.uniprot.txt index e7610db9..4591055e 100644 --- a/annotationPipeline/src/test/resources/expected/corner_cases.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/corner_cases.uniprot.txt @@ -1,5 +1,5 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.mskcc.txt b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.mskcc.txt index e7b8c584..cf94d48f 100644 --- a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.mskcc.txt +++ b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.mskcc.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000358026.2:c.3727C>G p.Arg1243Gly p.R1243G ENST00000358026 NM_001128849.1 1243 Cgg/Ggg 26/36 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000358026.2:c.3727C>G p.Arg1243Gly p.R1243G ENST00000358026 NM_001128849.1 1243 Cgg/Ggg 26/36 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.nucleotide_context.txt b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.nucleotide_context.txt index e92ddf86..d3b8557b 100644 --- a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.nucleotide_context.txt +++ b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.nucleotide_context.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 CAC CGC SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 GGC GAC SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 TCT TGT SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 CCG CAG SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 GTG GCG SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 CCG CTG SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 CGA CAA SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 GCA GTA SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 CGG CAG SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 GCC GAC SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 TCC TTC SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 CGG CAG SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 CGG CAG SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 TCG TTG SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 GCC GTC SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 CTC CAC SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 TCC TGC SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 CCA CGA SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 GTC GAC SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 CGA CAA SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 GTT GCT SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 TCT TAT SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 ACG AGG SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 ATT ACT SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 GCA GAA SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 GGG GCG SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 CGC CAC SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 TAT TGT SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 TGC TAC SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 AAT ACT SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 GGT GCT SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 GCC GAC SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 AGA ATA SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 TCA TGA SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 TCA TGA SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 CGA CAA SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 AGA ACA SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 TCA TTA SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 TCA TTA SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 TCA TAA SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 TCT TGT SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 TCA TGA SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 TCA TGA SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 CGT CAT SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 CTT CCT SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 ATA ACA SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 ACG ATG SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 TCA TTA SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 AGA AAA SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 AGA AAA SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 TCC TTC SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 CGC CAC SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 GGC GTC SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 GTA GCA SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 GGA GTA SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 TGT TCT SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 TCT TTT SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 TCG TGG SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 CGG CAG SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 GAT GGT SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 CAT CGT SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 GTT GCT SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 AGG AAG SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 TGG TCG SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 TCA TGA SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 GCG GGG SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 CGT CAT SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 GAG GTG SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 ATT AGT SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 AGA ACA SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 GGA GCA SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 CCA CTA SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 TCC TTC SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 TCA TGA SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 TCT TGT SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri genomic_location_explanation Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 CAC CGC SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 GGC GAC SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 TCT TGT SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 CCG CAG SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 GTG GCG SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 CCG CTG SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 CGA CAA SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 GCA GTA SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 CGG CAG SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 GCC GAC SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 TCC TTC SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 CGG CAG SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 CGG CAG SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 TCG TTG SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 GCC GTC SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 CTC CAC SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 TCC TGC SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 CCA CGA SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 GTC GAC SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 CGA CAA SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 GTT GCT SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 TCT TAT SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 ACG AGG SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 ATT ACT SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 GCA GAA SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 GGG GCG SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 CGC CAC SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 AGG AAG SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 TAT TGT SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 TGC TAC SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 AAT ACT SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 GGT GCT SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 GCC GAC SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 AGA ATA SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 TCA TGA SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 TCA TGA SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 CGA CAA SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 AGA ACA SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 TCA TTA SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 TCA TTA SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 TCA TAA SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 TCT TGT SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 TCA TGA SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 TCA TGA SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 CGT CAT SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 CTT CCT SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 ATA ACA SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 ACG ATG SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 TCA TTA SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 AGA AAA SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 AGA AAA SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 TCC TTC SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 AGG AAG SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 CGC CAC SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 GGC GTC SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 GTA GCA SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 GGA GTA SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 TGT TCT SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 TCT TTT SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 TCG TGG SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 CGG CAG SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 GAT GGT SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 CAT CGT SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 GTT GCT SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 AGG AAG SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 TGG TCG SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 TCA TGA SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 GCG GGG SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 CGT CAT SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 GAG GTG SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 ATT AGT SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 AGA ACA SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 GGA GCA SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 AGG AAG SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 CCA CTA SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 TCC TTC SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 TCA TGA SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 TCT TGT SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.txt b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.txt index b9fcab5a..46f5c9f5 100644 --- a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/minimal_example.uniprot.txt b/annotationPipeline/src/test/resources/expected/minimal_example.uniprot.txt index 6d114d38..0f0198aa 100644 --- a/annotationPipeline/src/test/resources/expected/minimal_example.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/minimal_example.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS -EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS +EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 Start position changes from 55242467 to 55242468 is attributed to the presence of common bases A. Reference allele changes from AATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases A. Variant allele changes from AGCAA to GCAA is attributed to the presence of common bases A. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/minimal_example_no_strip_off_matching_bases.expected.txt b/annotationPipeline/src/test/resources/expected/minimal_example_no_strip_off_matching_bases.expected.txt index 0647ccb5..854702c6 100644 --- a/annotationPipeline/src/test/resources/expected/minimal_example_no_strip_off_matching_bases.expected.txt +++ b/annotationPipeline/src/test/resources/expected/minimal_example_no_strip_off_matching_bases.expected.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS -EGFR 1956 GRCh37 7 55242466 55242486 + protein_altering_variant In_Frame_Del DEL GAATTAAGAGAAGCAACATCT GAGCAA GAGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS +EGFR 1956 GRCh37 7 55242466 55242486 + protein_altering_variant In_Frame_Del DEL GAATTAAGAGAAGCAACATCT GAGCAA GAGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 Start position changes from 55242466 to 55242468 is attributed to the presence of common bases GA. Reference allele changes from GAATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases GA. Variant allele changes from GAGCAA to GCAA is attributed to the presence of common bases GA. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/minimal_example_strip_off_first_matching_bases.expected.txt b/annotationPipeline/src/test/resources/expected/minimal_example_strip_off_first_matching_bases.expected.txt index 1e40f2b3..91fb2ba4 100644 --- a/annotationPipeline/src/test/resources/expected/minimal_example_strip_off_first_matching_bases.expected.txt +++ b/annotationPipeline/src/test/resources/expected/minimal_example_strip_off_first_matching_bases.expected.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS -EGFR 1956 GRCh37 7 55242467 55242486 + protein_altering_variant In_Frame_Del DEL AATTAAGAGAAGCAACATCT GAGCAA AGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS +EGFR 1956 GRCh37 7 55242467 55242486 + protein_altering_variant In_Frame_Del DEL AATTAAGAGAAGCAACATCT GAGCAA AGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 Start position changes from 55242466 to 55242468 is attributed to the presence of common bases GA. Reference allele changes from GAATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases GA. Variant allele changes from GAGCAA to GCAA is attributed to the presence of common bases GA. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/my_variant_info_corner_cases.uniprot.txt b/annotationPipeline/src/test/resources/expected/my_variant_info_corner_cases.uniprot.txt index ceae03b2..f26d5696 100644 --- a/annotationPipeline/src/test/resources/expected/my_variant_info_corner_cases.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/my_variant_info_corner_cases.uniprot.txt @@ -1,4 +1,4 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF Annotation_Status -BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 0.0288928 0.0431947 0.0336575 0.012004 0.0438969 0.00355757 0.0178879 0.0324421 0.0705371 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF genomic_location_explanation Annotation_Status +BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 0.0288928 0.0431947 0.0336575 0.012004 0.0438969 0.00355757 0.0178879 0.0324421 0.0705371 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/output_contains_original_genomic_location.expected.txt b/annotationPipeline/src/test/resources/expected/output_contains_original_genomic_location.expected.txt index 3374cd48..4345c378 100644 --- a/annotationPipeline/src/test/resources/expected/output_contains_original_genomic_location.expected.txt +++ b/annotationPipeline/src/test/resources/expected/output_contains_original_genomic_location.expected.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 3 178916939 TAGGCAACCGTGA 178916927 G SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 7 55220240 G 55220240 T SUCCESS -EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 7 55242486 AATTAAGAGAAGCAACATCT 55242467 AGCAA SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 genomic_location_explanation Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 3 178916939 TAGGCAACCGTGA 178916927 G SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 7 55220240 G 55220240 T SUCCESS +EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 7 55242486 AATTAAGAGAAGCAACATCT 55242467 AGCAA Start position changes from 55242467 to 55242468 is attributed to the presence of common bases A. Reference allele changes from AATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases A. Variant allele changes from AGCAA to GCAA is attributed to the presence of common bases A. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/test_ignore_original_genomic_location.expected.txt b/annotationPipeline/src/test/resources/expected/test_ignore_original_genomic_location.expected.txt index 5a8fab89..4b409183 100644 --- a/annotationPipeline/src/test/resources/expected/test_ignore_original_genomic_location.expected.txt +++ b/annotationPipeline/src/test/resources/expected/test_ignore_original_genomic_location.expected.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 3 178916939 TAGGCAACCGTGA 178916927 G G SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 7 55220240 G 55220240 T T SUCCESS -EGFR 1956 GRCh37 7 55242466 55242486 + protein_altering_variant In_Frame_Del DEL GAATTAAGAGAAGCAACATCT GAGCAA GAGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 7 55242486 ATTAAGAGAAGCAACATCT 55242468 GCAA GCAA SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 genomic_location_explanation Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 3 178916939 TAGGCAACCGTGA 178916927 G G SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 7 55220240 G 55220240 T T SUCCESS +EGFR 1956 GRCh37 7 55242466 55242486 + protein_altering_variant In_Frame_Del DEL GAATTAAGAGAAGCAACATCT GAGCAA GAGCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 7 55242486 ATTAAGAGAAGCAACATCT 55242468 GCAA GCAA Start position changes from 55242466 to 55242468 is attributed to the presence of common bases GA. Reference allele changes from GAATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases GA. Variant allele changes from GAGCAA to GCAA is attributed to the presence of common bases GA. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/test_output_format_extended.expected.txt b/annotationPipeline/src/test/resources/expected/test_output_format_extended.expected.txt index c9e6cb0a..d33e6f60 100644 --- a/annotationPipeline/src/test/resources/expected/test_output_format_extended.expected.txt +++ b/annotationPipeline/src/test/resources/expected/test_output_format_extended.expected.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer HGVSp_Short t_alt_count t_ref_count n_alt_count n_ref_count A B C Codons Consequence D Exon_Number HGVSc HGVSp Protein_position RefSeq Transcript_ID Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + In_Frame_Del DEL TAGGCAACCGTGA G G p.V105_E109delinsG gTAGGCAACCGTGAa/gGa protein_altering_variant 2/21 ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly 105 NM_006218.2 ENST00000263967 SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + Splice_Region SNP G T T p.X210_splice ctG/ctT splice_region_variant,synonymous_variant 6/28 ENST00000275493.2:c.630G>T 210 NM_005228.3 ENST00000275493 SUCCESS -EGFR 1956 GRCh37 7 55242468 55242486 + In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA p.L747_S752delinsQ gaATTAAGAGAAGCAACATCT/gaGCAA protein_altering_variant 19/28 ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln 746 NM_005228.3 ENST00000275493 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer HGVSp_Short t_alt_count t_ref_count n_alt_count n_ref_count A B C Codons Consequence D Exon_Number HGVSc HGVSp Protein_position RefSeq Transcript_ID genomic_location_explanation Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + In_Frame_Del DEL TAGGCAACCGTGA G G p.V105_E109delinsG gTAGGCAACCGTGAa/gGa protein_altering_variant 2/21 ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly 105 NM_006218.2 ENST00000263967 SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + Splice_Region SNP G T T p.X210_splice ctG/ctT splice_region_variant,synonymous_variant 6/28 ENST00000275493.2:c.630G>T 210 NM_005228.3 ENST00000275493 SUCCESS +EGFR 1956 GRCh37 7 55242468 55242486 + In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA p.L747_S752delinsQ gaATTAAGAGAAGCAACATCT/gaGCAA protein_altering_variant 19/28 ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln 746 NM_005228.3 ENST00000275493 Start position changes from 55242467 to 55242468 is attributed to the presence of common bases A. Reference allele changes from AATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases A. Variant allele changes from AGCAA to GCAA is attributed to the presence of common bases A. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/test_output_format_minimal.expected.txt b/annotationPipeline/src/test/resources/expected/test_output_format_minimal.expected.txt index 313f781e..2dfb72d6 100644 --- a/annotationPipeline/src/test/resources/expected/test_output_format_minimal.expected.txt +++ b/annotationPipeline/src/test/resources/expected/test_output_format_minimal.expected.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 BAM_File Center Codons Consequence Entrez_Gene_Id Exon_Number HGVSc HGVSp HGVSp_Short Hugo_Symbol Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Matched_Norm_Sample_Barcode Mutation_Status NCBI_Build Protein_position RefSeq Score Sequence_Source Sequencer Sequencing_Phase Strand Transcript_ID Tumor_Sample_Barcode Tumor_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Validation_Method Validation_Status Variant_Classification Variant_Type Verification_Status dbSNP_RS dbSNP_Val_Status n_alt_count n_ref_count t_alt_count t_ref_count Annotation_Status -3 178916927 178916939 TAGGCAACCGTGA G gTAGGCAACCGTGAa/gGa protein_altering_variant 5290 2/21 ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG PIK3CA GRCh37 105 NM_006218.2 + ENST00000263967 G In_Frame_Del DEL SUCCESS -7 55220240 55220240 G T ctG/ctT splice_region_variant,synonymous_variant 1956 6/28 ENST00000275493.2:c.630G>T p.X210_splice EGFR GRCh37 210 NM_005228.3 + ENST00000275493 T Splice_Region SNP SUCCESS -7 55242468 55242486 ATTAAGAGAAGCAACATCT AGCAA gaATTAAGAGAAGCAACATCT/gaGCAA protein_altering_variant 1956 19/28 ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ EGFR GRCh37 746 NM_005228.3 + ENST00000275493 GCAA In_Frame_Del DEL SUCCESS +Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 BAM_File Center Codons Consequence Entrez_Gene_Id Exon_Number HGVSc HGVSp HGVSp_Short Hugo_Symbol Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Matched_Norm_Sample_Barcode Mutation_Status NCBI_Build Protein_position RefSeq Score Sequence_Source Sequencer Sequencing_Phase Strand Transcript_ID Tumor_Sample_Barcode Tumor_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Validation_Method Validation_Status Variant_Classification Variant_Type Verification_Status dbSNP_RS dbSNP_Val_Status genomic_location_explanation n_alt_count n_ref_count t_alt_count t_ref_count Annotation_Status +3 178916927 178916939 TAGGCAACCGTGA G gTAGGCAACCGTGAa/gGa protein_altering_variant 5290 2/21 ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG PIK3CA GRCh37 105 NM_006218.2 + ENST00000263967 G In_Frame_Del DEL SUCCESS +7 55220240 55220240 G T ctG/ctT splice_region_variant,synonymous_variant 1956 6/28 ENST00000275493.2:c.630G>T p.X210_splice EGFR GRCh37 210 NM_005228.3 + ENST00000275493 T Splice_Region SNP SUCCESS +7 55242468 55242486 ATTAAGAGAAGCAACATCT AGCAA gaATTAAGAGAAGCAACATCT/gaGCAA protein_altering_variant 1956 19/28 ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ EGFR GRCh37 746 NM_005228.3 + ENST00000275493 GCAA In_Frame_Del DEL Start position changes from 55242467 to 55242468 is attributed to the presence of common bases A. Reference allele changes from AATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases A. Variant allele changes from AGCAA to GCAA is attributed to the presence of common bases A. SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/vcf2maf_tests.mskcc.txt b/annotationPipeline/src/test/resources/expected/vcf2maf_tests.mskcc.txt index 1863e890..844bfe03 100644 --- a/annotationPipeline/src/test/resources/expected/vcf2maf_tests.mskcc.txt +++ b/annotationPipeline/src/test/resources/expected/vcf2maf_tests.mskcc.txt @@ -1,20 +1,20 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc #version 2.4 -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number n_depth t_depth Annotation_Status -MTOR 0 . GRCh37 1 11290179 11290179 + intron_variant Intron DEL A A - rs35067541 TUMOR NORMAL A A 10 10 30 5 ENST00000361445.4:c.2779+803del p.*927* ENST00000361445 NM_004958.3 35 20 SUCCESS -Unknown 0 . GRCh37 1 15557977 15557978 + IGR DNP TG TG CA TUMOR NORMAL TG TG 11 5 21 1 22 16 SUCCESS -CHD1L 0 . GRCh37 1 146728217 146728217 + splice_donor_variant Splice_Site SNP G G A rs942221386 TUMOR NORMAL G G 19 21 42 0 ENST00000369258.4:c.494+1G>A p.X165_splice ENST00000369258 NM_001256336.1 165 42 40 SUCCESS -INHA 0 . GRCh37 2 220439700 220439701 + frameshift_variant Frame_Shift_Ins INS - - CT TUMOR NORMAL - - 21 72 51 0 ENST00000243786.2:c.562_563dup p.Leu189CysfsTer2 p.L189Cfs*2 ENST00000243786 NM_002191.3 185 gct/gCTct 2/2 51 93 SUCCESS -BAP1 0 . GRCh37 3 52437427 52437448 + splice_donor_variant,coding_sequence_variant,intron_variant Splice_Site DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA 10 10 11 0 ENST00000460680.1:c.1713_1729+5del p.X571_splice ENST00000460680 NM_004656.3 571 13/17 11 20 SUCCESS -BAP1 0 . GRCh37 3 52437702 52437708 + frameshift_variant Frame_Shift_Del DEL TGGGTGA TGGGTGA - TUMOR NORMAL TGGGTGA TGGGTGA 10 10 11 0 ENST00000460680.1:c.1453_1459del p.Ser485ProfsTer84 p.S485Pfs*84 ENST00000460680 NM_004656.3 485 TCACCCAcc/cc 13/17 11 20 SUCCESS -BAP1 0 . GRCh37 3 52443789 52443850 + splice_region_variant,intron_variant Splice_Region DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC 10 10 11 0 ENST00000460680.1:c.37+8_38-30del p.X13_splice ENST00000460680 NM_004656.3 13 11 20 SUCCESS -PIK3CA 0 . GRCh37 3 178928219 178928220 + protein_altering_variant,splice_region_variant In_Frame_Ins INS - - ATA TUMOR NORMAL - - 21 22 11 0 ENST00000263967.3:c.1406_1407insTAA p.Glu469delinsAspLys p.E469delinsDK ENST00000263967 NM_006218.2 469 gaa/gATAaa 9/21 11 43 SUCCESS -PIK3CA 0 . GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G - A rs104886003 TUMOR NORMAL G G 21 22 11 0 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 11 43 SUCCESS -TERT 0 . GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 TUMOR NORMAL G G 10 10 11 0 ENST00000310581 NM_198253.2 11 20 SUCCESS -TERT 0 . GRCh37 5 1295250 1295250 + upstream_gene_variant 5'Flank SNP G G A rs1561215364 TUMOR NORMAL G G 10 10 11 0 ENST00000310581 NM_198253.2 11 20 SUCCESS -MAP3K1 0 . GRCh37 5 56177849 56177851 + inframe_deletion In_Frame_Del DEL CAA CAA - rs5868032 TUMOR NORMAL CAA CAA 34 16 46 0 ENST00000399503.3:c.2845_2847del p.Thr949del p.T949del ENST00000399503 NM_005921.1 941 tCAAca/tca 14/20 46 50 SUCCESS -CCND3 0 . GRCh37 6 41903782 41903783 + missense_variant Missense_Mutation DNP AG AG CA rs386700585 TUMOR NORMAL AG AG 28 22 48 0 ENST00000372991.4:c.774_775delinsTG p.Ser259Ala p.S259A ENST00000372991 NM_001760.3 258 gcCTct/gcTGct 5/5 48 50 SUCCESS -MET 0 . GRCh37 7 116412043 116412043 + missense_variant,splice_region_variant Missense_Mutation SNP G G C TUMOR NORMAL G G 25 22 98 1 ENST00000397752.3:c.3028G>C p.Asp1010His p.D1010H ENST00000397752 NM_000245.2 1010 Gat/Cat 14/21 99 47 SUCCESS -FLT3 0 . GRCh37 13 28608242 28608243 + inframe_insertion In_Frame_Ins INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG TUMOR NORMAL - - 10 10 11 0 ENST00000241453.7:c.1813_1814insCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGT p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu p.E604_F605insSPRGGNEYFYVDFREYEYDLKWE ENST00000241453 NM_004119.2 605 ttt/tCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGTtt 14/24 11 20 SUCCESS -TP53 0 . GRCh37 17 7579312 7579312 + splice_region_variant,synonymous_variant Splice_Region SNP C C A rs55863639 TUMOR NORMAL C C 20 22 18 1 ENST00000269305.4:c.375G>T p.X125_splice ENST00000269305 NM_001126112.2 125 acG/acT 4/11 19 42 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation n_depth t_depth Annotation_Status +MTOR 2475 . GRCh37 1 11290179 11290179 + intron_variant Intron DEL A A - rs35067541 TUMOR NORMAL A A 10 10 30 5 ENST00000361445.4:c.2779+803del p.*927* ENST00000361445 NM_004958.3 35 20 SUCCESS +Unknown 0 . GRCh37 1 15557977 15557978 + IGR DNP TG TG CA TUMOR NORMAL TG TG 11 5 21 1 22 16 SUCCESS +CHD1L 9557 . GRCh37 1 146728217 146728217 + splice_donor_variant Splice_Site SNP G G A rs942221386 TUMOR NORMAL G G 19 21 42 0 ENST00000369258.4:c.494+1G>A p.X165_splice ENST00000369258 NM_001256336.1 165 42 40 SUCCESS +INHA 3623 . GRCh37 2 220439700 220439701 + frameshift_variant Frame_Shift_Ins INS - - CT TUMOR NORMAL - - 21 72 51 0 ENST00000243786.2:c.562_563dup p.Leu189CysfsTer2 p.L189Cfs*2 ENST00000243786 NM_002191.3 185 gct/gCTct 2/2 51 93 SUCCESS +BAP1 8314 . GRCh37 3 52437427 52437448 + splice_donor_variant,coding_sequence_variant,intron_variant Splice_Site DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA 10 10 11 0 ENST00000460680.1:c.1713_1729+5del p.X571_splice ENST00000460680 NM_004656.3 571 13/17 11 20 SUCCESS +BAP1 8314 . GRCh37 3 52437702 52437708 + frameshift_variant Frame_Shift_Del DEL TGGGTGA TGGGTGA - TUMOR NORMAL TGGGTGA TGGGTGA 10 10 11 0 ENST00000460680.1:c.1453_1459del p.Ser485ProfsTer84 p.S485Pfs*84 ENST00000460680 NM_004656.3 485 TCACCCAcc/cc 13/17 11 20 SUCCESS +BAP1 8314 . GRCh37 3 52443789 52443850 + splice_region_variant,intron_variant Splice_Region DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC 10 10 11 0 ENST00000460680.1:c.37+8_38-30del p.X13_splice ENST00000460680 NM_004656.3 13 11 20 SUCCESS +PIK3CA 5290 . GRCh37 3 178928219 178928220 + protein_altering_variant,splice_region_variant In_Frame_Ins INS - - ATA TUMOR NORMAL - - 21 22 11 0 ENST00000263967.3:c.1406_1407insTAA p.Glu469delinsAspLys p.E469delinsDK ENST00000263967 NM_006218.2 469 gaa/gATAaa 9/21 11 43 SUCCESS +PIK3CA 5290 . GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G - A rs104886003 TUMOR NORMAL G G 21 22 11 0 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 11 43 SUCCESS +TERT 7015 . GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 TUMOR NORMAL G G 10 10 11 0 ENST00000310581 NM_198253.2 11 20 SUCCESS +TERT 7015 . GRCh37 5 1295250 1295250 + upstream_gene_variant 5'Flank SNP G G A rs1561215364 TUMOR NORMAL G G 10 10 11 0 ENST00000310581 NM_198253.2 11 20 SUCCESS +MAP3K1 4214 . GRCh37 5 56177849 56177851 + inframe_deletion In_Frame_Del DEL CAA CAA - rs5868032 TUMOR NORMAL CAA CAA 34 16 46 0 ENST00000399503.3:c.2845_2847del p.Thr949del p.T949del ENST00000399503 NM_005921.1 941 tCAAca/tca 14/20 46 50 SUCCESS +CCND3 896 . GRCh37 6 41903782 41903783 + missense_variant Missense_Mutation DNP AG AG CA rs386700585 TUMOR NORMAL AG AG 28 22 48 0 ENST00000372991.4:c.774_775delinsTG p.Ser259Ala p.S259A ENST00000372991 NM_001760.3 258 gcCTct/gcTGct 5/5 48 50 SUCCESS +MET 4233 . GRCh37 7 116412043 116412043 + missense_variant,splice_region_variant Missense_Mutation SNP G G C TUMOR NORMAL G G 25 22 98 1 ENST00000397752.3:c.3028G>C p.Asp1010His p.D1010H ENST00000397752 NM_000245.2 1010 Gat/Cat 14/21 99 47 SUCCESS +FLT3 2322 . GRCh37 13 28608242 28608243 + inframe_insertion In_Frame_Ins INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG TUMOR NORMAL - - 10 10 11 0 ENST00000241453.7:c.1813_1814insCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGT p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu p.E604_F605insSPRGGNEYFYVDFREYEYDLKWE ENST00000241453 NM_004119.2 605 ttt/tCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGTtt 14/24 11 20 SUCCESS +TP53 7157 . GRCh37 17 7579312 7579312 + splice_region_variant,synonymous_variant Splice_Region SNP C C A rs55863639 TUMOR NORMAL C C 20 22 18 1 ENST00000269305.4:c.375G>T p.X125_splice ENST00000269305 NM_001126112.2 125 acG/acT 4/11 19 42 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/vcf2maf_tests.uniprot.txt b/annotationPipeline/src/test/resources/expected/vcf2maf_tests.uniprot.txt index 7f7fea69..01a427b3 100644 --- a/annotationPipeline/src/test/resources/expected/vcf2maf_tests.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/vcf2maf_tests.uniprot.txt @@ -1,20 +1,20 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot #version 2.4 -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number n_depth t_depth Annotation_Status -MTOR 0 . GRCh37 1 11290179 11290179 + intron_variant Intron DEL A A - rs35067541 TUMOR NORMAL A A 10 10 30 5 ENST00000361445.4:c.2779+803del p.*927* ENST00000361445 NM_004958.3 35 20 SUCCESS -Unknown 0 . GRCh37 1 15557977 15557978 + IGR DNP TG TG CA TUMOR NORMAL TG TG 11 5 21 1 22 16 SUCCESS -CHD1L 0 . GRCh37 1 146728217 146728217 + splice_donor_variant Splice_Site SNP G G A rs942221386 TUMOR NORMAL G G 19 21 42 0 ENST00000369258.4:c.494+1G>A p.X165_splice ENST00000369258 NM_001256336.1 165 42 40 SUCCESS -INHA 0 . GRCh37 2 220439700 220439701 + frameshift_variant Frame_Shift_Ins INS - - CT TUMOR NORMAL - - 21 72 51 0 ENST00000243786.2:c.562_563dup p.Leu189CysfsTer2 p.L189Cfs*2 ENST00000243786 NM_002191.3 185 gct/gCTct 2/2 51 93 SUCCESS -BAP1 0 . GRCh37 3 52437427 52437448 + splice_donor_variant,coding_sequence_variant,intron_variant Splice_Site DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA 10 10 11 0 ENST00000460680.1:c.1713_1729+5del p.X571_splice ENST00000460680 NM_004656.3 571 13/17 11 20 SUCCESS -BAP1 0 . GRCh37 3 52437702 52437708 + frameshift_variant Frame_Shift_Del DEL TGGGTGA TGGGTGA - TUMOR NORMAL TGGGTGA TGGGTGA 10 10 11 0 ENST00000460680.1:c.1453_1459del p.Ser485ProfsTer84 p.S485Pfs*84 ENST00000460680 NM_004656.3 485 TCACCCAcc/cc 13/17 11 20 SUCCESS -BAP1 0 . GRCh37 3 52443789 52443850 + splice_region_variant,intron_variant Splice_Region DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC 10 10 11 0 ENST00000460680.1:c.37+8_38-30del p.X13_splice ENST00000460680 NM_004656.3 13 11 20 SUCCESS -PIK3CA 0 . GRCh37 3 178928219 178928220 + protein_altering_variant,splice_region_variant In_Frame_Ins INS - - ATA TUMOR NORMAL - - 21 22 11 0 ENST00000263967.3:c.1406_1407insTAA p.Glu469delinsAspLys p.E469delinsDK ENST00000263967 NM_006218.2 469 gaa/gATAaa 9/21 11 43 SUCCESS -PIK3CA 0 . GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G - A rs104886003 TUMOR NORMAL G G 21 22 11 0 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 11 43 SUCCESS -TERT 0 . GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 TUMOR NORMAL G G 10 10 11 0 ENST00000310581 NM_198253.2 11 20 SUCCESS -TERT 0 . GRCh37 5 1295250 1295250 + upstream_gene_variant 5'Flank SNP G G A rs1561215364 TUMOR NORMAL G G 10 10 11 0 ENST00000310581 NM_198253.2 11 20 SUCCESS -MAP3K1 0 . GRCh37 5 56177849 56177851 + inframe_deletion In_Frame_Del DEL CAA CAA - rs5868032 TUMOR NORMAL CAA CAA 34 16 46 0 ENST00000399503.3:c.2845_2847del p.Thr949del p.T949del ENST00000399503 NM_005921.1 941 tCAAca/tca 14/20 46 50 SUCCESS -CCND3 0 . GRCh37 6 41903782 41903783 + missense_variant Missense_Mutation DNP AG AG CA rs386700585 TUMOR NORMAL AG AG 28 22 48 0 ENST00000372991.4:c.774_775delinsTG p.Ser259Ala p.S259A ENST00000372991 NM_001760.3 258 gcCTct/gcTGct 5/5 48 50 SUCCESS -MET 0 . GRCh37 7 116412043 116412043 + missense_variant,splice_region_variant Missense_Mutation SNP G G C TUMOR NORMAL G G 25 22 98 1 ENST00000397752.3:c.3028G>C p.Asp1010His p.D1010H ENST00000397752 NM_000245.2 1010 Gat/Cat 14/21 99 47 SUCCESS -FLT3 0 . GRCh37 13 28608242 28608243 + inframe_insertion In_Frame_Ins INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG TUMOR NORMAL - - 10 10 11 0 ENST00000241453.7:c.1813_1814insCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGT p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu p.E604_F605insSPRGGNEYFYVDFREYEYDLKWE ENST00000241453 NM_004119.2 605 ttt/tCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGTtt 14/24 11 20 SUCCESS -TP53 0 . GRCh37 17 7579312 7579312 + splice_region_variant,synonymous_variant Splice_Region SNP C C A rs55863639 TUMOR NORMAL C C 20 22 18 1 ENST00000269305.4:c.375G>T p.X125_splice ENST00000269305 NM_001126112.2 125 acG/acT 4/11 19 42 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation n_depth t_depth Annotation_Status +MTOR 2475 . GRCh37 1 11290179 11290179 + intron_variant Intron DEL A A - rs35067541 TUMOR NORMAL A A 10 10 30 5 ENST00000361445.4:c.2779+803del p.*927* ENST00000361445 NM_004958.3 35 20 SUCCESS +Unknown 0 . GRCh37 1 15557977 15557978 + IGR DNP TG TG CA TUMOR NORMAL TG TG 11 5 21 1 22 16 SUCCESS +CHD1L 9557 . GRCh37 1 146728217 146728217 + splice_donor_variant Splice_Site SNP G G A rs942221386 TUMOR NORMAL G G 19 21 42 0 ENST00000369258.4:c.494+1G>A p.X165_splice ENST00000369258 NM_001256336.1 165 42 40 SUCCESS +INHA 3623 . GRCh37 2 220439700 220439701 + frameshift_variant Frame_Shift_Ins INS - - CT TUMOR NORMAL - - 21 72 51 0 ENST00000243786.2:c.562_563dup p.Leu189CysfsTer2 p.L189Cfs*2 ENST00000243786 NM_002191.3 185 gct/gCTct 2/2 51 93 SUCCESS +BAP1 8314 . GRCh37 3 52437427 52437448 + splice_donor_variant,coding_sequence_variant,intron_variant Splice_Site DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA 10 10 11 0 ENST00000460680.1:c.1713_1729+5del p.X571_splice ENST00000460680 NM_004656.3 571 13/17 11 20 SUCCESS +BAP1 8314 . GRCh37 3 52437702 52437708 + frameshift_variant Frame_Shift_Del DEL TGGGTGA TGGGTGA - TUMOR NORMAL TGGGTGA TGGGTGA 10 10 11 0 ENST00000460680.1:c.1453_1459del p.Ser485ProfsTer84 p.S485Pfs*84 ENST00000460680 NM_004656.3 485 TCACCCAcc/cc 13/17 11 20 SUCCESS +BAP1 8314 . GRCh37 3 52443789 52443850 + splice_region_variant,intron_variant Splice_Region DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC 10 10 11 0 ENST00000460680.1:c.37+8_38-30del p.X13_splice ENST00000460680 NM_004656.3 13 11 20 SUCCESS +PIK3CA 5290 . GRCh37 3 178928219 178928220 + protein_altering_variant,splice_region_variant In_Frame_Ins INS - - ATA TUMOR NORMAL - - 21 22 11 0 ENST00000263967.3:c.1406_1407insTAA p.Glu469delinsAspLys p.E469delinsDK ENST00000263967 NM_006218.2 469 gaa/gATAaa 9/21 11 43 SUCCESS +PIK3CA 5290 . GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G - A rs104886003 TUMOR NORMAL G G 21 22 11 0 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 11 43 SUCCESS +TERT 7015 . GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 TUMOR NORMAL G G 10 10 11 0 ENST00000310581 NM_198253.2 11 20 SUCCESS +TERT 7015 . GRCh37 5 1295250 1295250 + upstream_gene_variant 5'Flank SNP G G A rs1561215364 TUMOR NORMAL G G 10 10 11 0 ENST00000310581 NM_198253.2 11 20 SUCCESS +MAP3K1 4214 . GRCh37 5 56177849 56177851 + inframe_deletion In_Frame_Del DEL CAA CAA - rs5868032 TUMOR NORMAL CAA CAA 34 16 46 0 ENST00000399503.3:c.2845_2847del p.Thr949del p.T949del ENST00000399503 NM_005921.1 941 tCAAca/tca 14/20 46 50 SUCCESS +CCND3 896 . GRCh37 6 41903782 41903783 + missense_variant Missense_Mutation DNP AG AG CA rs386700585 TUMOR NORMAL AG AG 28 22 48 0 ENST00000372991.4:c.774_775delinsTG p.Ser259Ala p.S259A ENST00000372991 NM_001760.3 258 gcCTct/gcTGct 5/5 48 50 SUCCESS +MET 4233 . GRCh37 7 116412043 116412043 + missense_variant,splice_region_variant Missense_Mutation SNP G G C TUMOR NORMAL G G 25 22 98 1 ENST00000397752.3:c.3028G>C p.Asp1010His p.D1010H ENST00000397752 NM_000245.2 1010 Gat/Cat 14/21 99 47 SUCCESS +FLT3 2322 . GRCh37 13 28608242 28608243 + inframe_insertion In_Frame_Ins INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG TUMOR NORMAL - - 10 10 11 0 ENST00000241453.7:c.1813_1814insCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGT p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu p.E604_F605insSPRGGNEYFYVDFREYEYDLKWE ENST00000241453 NM_004119.2 605 ttt/tCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGTtt 14/24 11 20 SUCCESS +TP53 7157 . GRCh37 17 7579312 7579312 + splice_region_variant,synonymous_variant Splice_Region SNP C C A rs55863639 TUMOR NORMAL C C 20 22 18 1 ENST00000269305.4:c.375G>T p.X125_splice ENST00000269305 NM_001126112.2 125 acG/acT 4/11 19 42 SUCCESS diff --git a/test/data/corner_cases.out.mskcc.txt b/test/data/corner_cases.out.mskcc.txt index 70891097..c3be1839 100644 --- a/test/data/corner_cases.out.mskcc.txt +++ b/test/data/corner_cases.out.mskcc.txt @@ -1,5 +1,5 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS diff --git a/test/data/corner_cases.out.uniprot.txt b/test/data/corner_cases.out.uniprot.txt index e7610db9..4591055e 100644 --- a/test/data/corner_cases.out.uniprot.txt +++ b/test/data/corner_cases.out.uniprot.txt @@ -1,5 +1,5 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC GT GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS diff --git a/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt b/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt index fe245c40..890ed668 100644 --- a/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt +++ b/test/data/corner_cases.two_tumor_seq_allele.out.mskcc.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS -KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 Start position changes from 17796382 to 17796383 is attributed to the presence of common bases A. Reference allele changes from AC to C is attributed to the presence of common bases A. Variant allele changes from AAC to AC is attributed to the presence of common bases A. SUCCESS +KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 Start position changes from 17796381 to 17796382 is attributed to the presence of common bases A. Reference allele changes from AAC to AC is attributed to the presence of common bases A. Variant allele changes from AGT to GT is attributed to the presence of common bases A. SUCCESS diff --git a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt index 7b6ec286..ca9c576c 100644 --- a/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt +++ b/test/data/corner_cases.two_tumor_seq_allele.out.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS -KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS -PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 Start position changes from 17796382 to 17796383 is attributed to the presence of common bases A. Reference allele changes from AC to C is attributed to the presence of common bases A. Variant allele changes from AAC to AC is attributed to the presence of common bases A. SUCCESS +KMT2D 8085 GRCh37 12 49435045 49435045 + missense_variant Missense_Mutation SNP G C C rs758743247 ENST00000301067.7:c.6508C>G p.Gln2170Glu p.Q2170E ENST00000301067 NM_003482.3 2170 Caa/Gaa 31/54 SUCCESS +PCM1 5108 GRCh37 8 17796382 17796383 + missense_variant Missense_Mutation DNP AC AC GT rs754721723 ENST00000325083.8:c.476_477inv p.Asn159Ser p.N159S ENST00000325083 NM_006197.3 159 aAC/aGT 5/39 Start position changes from 17796381 to 17796382 is attributed to the presence of common bases A. Reference allele changes from AAC to AC is attributed to the presence of common bases A. Variant allele changes from AGT to GT is attributed to the presence of common bases A. SUCCESS diff --git a/test/data/data_mutations_extended_100.out.mskcc.txt b/test/data/data_mutations_extended_100.out.mskcc.txt index 08c535dc..cf94d48f 100644 --- a/test/data/data_mutations_extended_100.out.mskcc.txt +++ b/test/data/data_mutations_extended_100.out.mskcc.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 1.0.2 #isoform: mskcc -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS -AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS -PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS -POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000358026.2:c.3727C>G p.Arg1243Gly p.R1243G ENST00000358026 NM_001128849.1 1243 Cgg/Ggg 26/36 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS -MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS -IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000397332.2:c.851T>G p.Ile284Ser p.I284S ENST00000397332 NM_001033082.2 284 aTt/aGt 3/3 SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000358026.2:c.3727C>G p.Arg1243Gly p.R1243G ENST00000358026 NM_001128849.1 1243 Cgg/Ggg 26/36 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS diff --git a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt index 6bbae540..d3b8557b 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.nucleotide_context.txt @@ -1,102 +1,102 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri Annotation_Status -SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS -ALK GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 CAC CGC SUCCESS -PDCD1 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 GGC GAC SUCCESS -MAP3K1 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 TCT TGT SUCCESS -FLT4 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 CCG CAG SUCCESS -FLT4 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 GTG GCG SUCCESS -NOTCH4 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 CCG CTG SUCCESS -NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 CGA CAA SUCCESS -MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 GCA GTA SUCCESS -MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 CGG CAG SUCCESS -TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 GCC GAC SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 TCC TTC SUCCESS -TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 CGG CAG SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 CGG CAG SUCCESS -NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 TCG TTG SUCCESS -TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 GCC GTC SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 CTC CAC SUCCESS -CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 TCC TGC SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 CCA CGA SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 GTC GAC SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 CGA CAA SUCCESS -U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 GTT GCT SUCCESS -BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 TCT TAT SUCCESS -PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 ACG AGG SUCCESS -BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 ATT ACT SUCCESS -ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 GCA GAA SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 GGG GCG SUCCESS -IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 CGC CAC SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 TAT TGT SUCCESS -ABL1 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 TGC TAC SUCCESS -MYCL1 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 AAT ACT SUCCESS -POLE GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 GGT GCT SUCCESS -TP53 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 GCC GAC SUCCESS -NCOR1 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 AGA ATA SUCCESS -ARID1A GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 TCA TGA SUCCESS -RYBP GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.938G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 TCA TGA SUCCESS -FAT1 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 CGA CAA SUCCESS -FGFR4 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 AGA ACA SUCCESS -BLM GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 TCA TTA SUCCESS -BLM GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 TCA TTA SUCCESS -BLM GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 TCA TAA SUCCESS -BLM GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 TCT TGT SUCCESS -BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 TCA TGA SUCCESS -BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 TCA TGA SUCCESS -CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 CGT CAT SUCCESS -KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 CTT CCT SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 ATA ACA SUCCESS -BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 ACG ATG SUCCESS -NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 TCA TTA SUCCESS -ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 AGA AAA SUCCESS -PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 AGA AAA SUCCESS -NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 TCC TTC SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 CGC CAC SUCCESS -FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 GGC GTC SUCCESS -NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 GTA GCA SUCCESS -CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 GGA GTA SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS -BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 TGT TCT SUCCESS -MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 TCT TTT SUCCESS -NOTCH4 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 TCG TGG SUCCESS -TP53 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 CGG CAG SUCCESS -TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 GAT GGT SUCCESS -TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS -PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 CAT CGT SUCCESS -PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 GTT GCT SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 AGG AAG SUCCESS -SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 TGG TCG SUCCESS -FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 TCA TGA SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 GCG GGG SUCCESS -TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS -EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 CGT CAT SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 SUCCESS -IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 ATT AGT SUCCESS -KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 AGA ACA SUCCESS -KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 GGA GCA SUCCESS -TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 AGG AAG SUCCESS -EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 CCA CTA SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 TCC TTC SUCCESS -FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 TCA TGA SUCCESS -FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 TCT TGT SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri genomic_location_explanation Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 CAC CGC SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 GGC GAC SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 TCT TGT SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 CCG CAG SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 GTG GCG SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 CCG CTG SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 CGA CAA SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 GCA GTA SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 CGG CAG SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 GCC GAC SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 TCC TTC SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 CGG CAG SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 CGG CAG SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 TCG TTG SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 GCC GTC SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 CTC CAC SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 TCC TGC SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 CCA CGA SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 GTC GAC SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 CGA CAA SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 GTT GCT SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 TCT TAT SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 ACG AGG SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 ATT ACT SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 GCA GAA SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 GGG GCG SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 CGC CAC SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 AGG AAG SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 TAT TGT SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 TGC TAC SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 AAT ACT SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 GGT GCT SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 GCC GAC SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 AGA ATA SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 TCA TGA SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 TCA TGA SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 CGA CAA SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 AGA ACA SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 TCA TTA SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 TCA TTA SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 TCA TAA SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 TCT TGT SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 TCA TGA SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 TCA TGA SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 CGT CAT SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 CTT CCT SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 ATA ACA SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 ACG ATG SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 TCA TTA SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 AGA AAA SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 AGA AAA SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 TCC TTC SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 AGG AAG SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 CGC CAC SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 GGC GTC SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 GTA GCA SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 GGA GTA SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 TGA TAA SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 TGT TCT SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 TCT TTT SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 TCG TGG SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 CGG CAG SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 GAT GGT SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 CCG CTG SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 CAT CGT SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 GTT GCT SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 AGG AAG SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 TGG TCG SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 TCA TGA SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 GCG GGG SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 CGT CAT SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 GAG GTG SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 ATT AGT SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 AGA ACA SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 GGA GCA SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 AGG AAG SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 CCA CTA SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 TCC TTC SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 TCA TGA SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 TCT TGT SUCCESS diff --git a/test/data/data_mutations_extended_100.out.uniprot.txt b/test/data/data_mutations_extended_100.out.uniprot.txt index f0ea20bd..46f5c9f5 100644 --- a/test/data/data_mutations_extended_100.out.uniprot.txt +++ b/test/data/data_mutations_extended_100.out.uniprot.txt @@ -1,102 +1,102 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS -ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS -PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS -MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS -FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS -FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS -NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS -NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS -KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS -KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS -TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS -AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS -TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS -NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS -TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS -ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS -CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS -U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS -BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS -LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS -CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS -PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS -BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS -ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS -PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS -IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS -CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS -ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS -MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS -POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS -TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS -NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS -ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS -RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS -FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS -FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS -BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS -BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS -BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS -BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS -BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS -BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS -CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS -KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS -BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS -TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS -NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS -ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS -PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS -NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS -BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS -FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS -NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS -CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS -PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS -MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS -NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS -TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS -TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS -TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS -PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS -PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS -SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS -MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS -PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS -FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS -TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 SUCCESS -IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS -KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS -KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS -TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS -EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS -FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS -FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +SPEN 23013 GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS +ALK 238 GRCh37 2 29543736 29543736 + missense_variant Missense_Mutation SNP A A G rs35093491 P-0000004-T01-IM3 180 13 ENST00000389048.3:c.1427T>C p.Val476Ala p.V476A ENST00000389048 NM_004304.4 476 gTg/gCg 7/29 SUCCESS +PDCD1 5133 GRCh37 2 242793433 242793433 + missense_variant Missense_Mutation SNP G G A rs2227982 P-0000004-T01-IM3 225 15 ENST00000334409.5:c.644C>T p.Ala215Val p.A215V ENST00000334409 NM_005018.2 215 gCc/gTc 5/5 SUCCESS +MAP3K1 4214 GRCh37 5 56177843 56177843 + missense_variant Missense_Mutation SNP C C G rs45556841 P-0000004-T01-IM3 370 12 ENST00000399503.3:c.2816C>G p.Ser939Cys p.S939C ENST00000399503 NM_005921.1 939 tCt/tGt 14/20 SUCCESS +FLT4 2324 GRCh37 5 180030313 180030313 + missense_variant Missense_Mutation SNP C C A rs307821 P-0000004-T01-IM3 360 25 ENST00000261937.6:c.3971G>T p.Arg1324Leu p.R1324L ENST00000261937 NM_182925.4 1324 cGg/cTg 30/30 SUCCESS +FLT4 2324 GRCh37 5 180051003 180051003 + missense_variant Missense_Mutation SNP T T C rs307826 P-0000004-T01-IM3 273 22 ENST00000261937.6:c.1480A>G p.Thr494Ala p.T494A ENST00000261937 NM_182925.4 494 Acg/Gcg 11/30 SUCCESS +NOTCH4 4855 GRCh37 6 32178570 32178570 + missense_variant Missense_Mutation SNP C C T rs17604492 P-0000004-T01-IM3 279 17 ENST00000375023.3:c.2824G>A p.Gly942Arg p.G942R ENST00000375023 NM_004557.3 942 Ggg/Agg 18/30 SUCCESS +NOTCH4 4855 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G A rs8192585 P-0000004-T01-IM3 207 11 ENST00000375023.3:c.731C>T p.Ser244Leu p.S244L ENST00000375023 NM_004557.3 244 tCg/tTg 4/30 SUCCESS +KMT2C 58508 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS +KMT2D 8085 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS +TSHR 7253 GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000541158.2:c.154C>A p.Pro52Thr p.P52T ENST00000541158 52 Ccc/Acc 2/11 SUCCESS +AKT1 207 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +TSC2 7249 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS +RNF43 54894 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +NOTCH3 4854 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS +TP53 7157 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS +ALK 238 GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +ESR1 2099 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +CDK4 1019 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +RNF43 54894 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS +GATA3 2625 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS +LATS1 9113 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS +LATS1 9113 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +U2AF1 7307 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS +BAP1 8314 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS +LATS2 26524 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS +CTNNB1 1499 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C A rs121913403 P-0000024-T01-IM3 965 280 ENST00000349496.5:c.110C>A p.Ser37Tyr p.S37Y ENST00000349496 NM_001904.3 37 tCt/tAt 3/15 SUCCESS +PTEN 5728 GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS +BCOR 54880 GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS +ARID1A 8289 GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS +PIK3R1 5295 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS +PTEN 5728 GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS +LATS1 9113 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +IKZF1 10320 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS +CUL3 8452 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS +ABL1 25 GRCh37 9 133750275 133750275 + missense_variant Missense_Mutation SNP G G A P-0000039-T01-IM3 197 27 ENST00000318560.5:c.1106G>A p.Cys369Tyr p.C369Y ENST00000318560 NM_005157.4 369 tGc/tAc 7/11 SUCCESS +MYCL 4610 GRCh37 1 40363378 40363378 + missense_variant Missense_Mutation SNP A A C P-0000037-T01-IM3 629 124 ENST00000372816.2:c.761T>G p.Ile254Ser p.I254S ENST00000372816 254 aTt/aGt 2/2 SUCCESS +POLE 5426 GRCh37 12 133202730 133202730 + missense_variant Missense_Mutation SNP G G C P-0000037-T01-IM3 650 145 ENST00000320574.5:c.6504C>G p.Asp2168Glu p.D2168E ENST00000320574 NM_006231.2 2168 gaC/gaG 46/49 SUCCESS +TP53 7157 GRCh37 17 7577534 7577534 + missense_variant Missense_Mutation SNP C C A rs28934571 P-0000037-T01-IM3 293 230 ENST00000269305.4:c.747G>T p.Arg249Ser p.R249S ENST00000269305 NM_001126112.2 249 agG/agT 7/11 SUCCESS +NCOR1 9611 GRCh37 17 15960850 15960850 + missense_variant Missense_Mutation SNP G G T P-0000037-T01-IM3 307 118 ENST00000268712.3:c.6370C>A p.Leu2124Ile p.L2124I ENST00000268712 NM_006311.3 2124 Ctt/Att 40/46 SUCCESS +ARID1A 8289 GRCh37 1 27023307 27023307 + stop_gained Nonsense_Mutation SNP C C G P-0000034-T01-IM3 133 27 ENST00000324856.7:c.413C>G p.Ser138Ter p.S138* ENST00000324856 NM_006015.4 138 tCa/tGa 1/20 SUCCESS +RYBP 23429 GRCh37 3 72427550 72427550 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 337 102 ENST00000477973.2:c.940G>C p.Asp314His p.D314H ENST00000477973 NM_012234.5 314 Gat/Cat 4/4 SUCCESS +FAT1 2195 GRCh37 4 187540074 187540074 + stop_gained Nonsense_Mutation SNP G G A rs921535768 P-0000034-T01-IM3 659 78 ENST00000441802.2:c.7666C>T p.Arg2556Ter p.R2556* ENST00000441802 NM_005245.3 2556 Cga/Tga 10/27 SUCCESS +FGFR4 2264 GRCh37 5 176518800 176518800 + missense_variant Missense_Mutation SNP G G C P-0000034-T01-IM3 126 24 ENST00000292408.4:c.718G>C p.Asp240His p.D240H ENST00000292408 NM_213647.1 240 Gat/Cat 6/18 SUCCESS +BLM 641 GRCh37 15 91292745 91292745 + stop_gained Nonsense_Mutation SNP C C T P-0000034-T01-IM3 721 59 ENST00000355112.3:c.247C>T p.Gln83Ter p.Q83* ENST00000355112 NM_000057.2 83 Cag/Tag 3/22 SUCCESS +BLM 641 GRCh37 15 91292809 91292809 + missense_variant Missense_Mutation SNP C C T rs367543030 P-0000034-T01-IM3 631 51 ENST00000355112.3:c.311C>T p.Ser104Leu p.S104L ENST00000355112 NM_000057.2 104 tCa/tTa 3/22 SUCCESS +BLM 641 GRCh37 15 91292815 91292815 + stop_gained Nonsense_Mutation SNP C C A P-0000034-T01-IM3 641 51 ENST00000355112.3:c.317C>A p.Ser106Ter p.S106* ENST00000355112 NM_000057.2 106 tCa/tAa 3/22 SUCCESS +BLM 641 GRCh37 15 91292904 91292904 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 685 44 ENST00000355112.3:c.406C>G p.Leu136Val p.L136V ENST00000355112 NM_000057.2 136 Ctc/Gtc 3/22 SUCCESS +BLM 641 GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 709 42 ENST00000355112.3:c.453C>G p.Ile151Met p.I151M ENST00000355112 NM_000057.2 151 atC/atG 3/22 SUCCESS +BLM 641 GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS +CIC 23152 GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS +KDM6A 7403 GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS +FOXP1 27086 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS +AKT1 207 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +BAP1 8314 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS +TP53 7157 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS +NRAS 4893 GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS +ATR 545 GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS +PIK3CA 5290 GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS +NOTCH3 4854 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS +PIK3R1 5295 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS +BAP1 8314 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS +FGFR4 2264 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS +NOTCH4 4855 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS +CDKN1A 1026 GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS +FGFR3 2261 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +PIK3CA 5290 GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS +BARD1 580 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS +MAP3K13 9175 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS +NOTCH4 4855 GRCh37 6 32172007 32172007 + missense_variant Missense_Mutation SNP C C G P-0000057-T01-IM3 411 164 ENST00000375023.3:c.3025G>C p.Glu1009Gln p.E1009Q ENST00000375023 NM_004557.3 1009 Gag/Cag 19/30 SUCCESS +TP53 7157 GRCh37 17 7574003 7574003 + stop_gained Nonsense_Mutation SNP G G A rs730882029 P-0000057-T01-IM3 442 261 ENST00000269305.4:c.1024C>T p.Arg342Ter p.R342* ENST00000269305 NM_001126112.2 342 Cga/Tga 10/11 SUCCESS +TP53 7157 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G rs760043106 P-0000058-T01-IM3 156 348 ENST00000269305.4:c.584T>C p.Ile195Thr p.I195T ENST00000269305 NM_001126112.2 195 aTc/aCc 6/11 SUCCESS +TP53 7157 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS +PIK3CA 5290 GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS +PTEN 5728 GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS +BRCA2 675 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +SMO 6608 GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS +MCL1 4170 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS +PIK3CA 5290 GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS +FAT1 2195 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS +SMARCA4 6597 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +TP53 7157 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS +EZH2 2146 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS +MDM2 4193 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 SUCCESS +IGF1R 3480 GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS +KEAP1 9817 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS +KDM5C 8242 GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS +TERT 7015 GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS +EPHB1 2047 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS +FGFR3 2261 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FAT1 2195 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS +FAT1 2195 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS diff --git a/test/data/immutable_columns_test.out.uniprot.txt b/test/data/immutable_columns_test.out.uniprot.txt index dd9f6ac6..ad4f246d 100644 --- a/test/data/immutable_columns_test.out.uniprot.txt +++ b/test/data/immutable_columns_test.out.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 3 178916939 TAGGCAACCGTGA 178916927 G SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 7 55220240 G 55220240 T SUCCESS -EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 7 55242486 AATTAAGAGAAGCAACATCT 55242467 AGCAA SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number IGNORE_Genome_Nexus_Original_Chromosome IGNORE_Genome_Nexus_Original_End_Position IGNORE_Genome_Nexus_Original_Reference_Allele IGNORE_Genome_Nexus_Original_Start_Position IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele1 IGNORE_Genome_Nexus_Original_Tumor_Seq_Allele2 genomic_location_explanation Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 3 178916939 TAGGCAACCGTGA 178916927 G SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 7 55220240 G 55220240 T SUCCESS +EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 7 55242486 AATTAAGAGAAGCAACATCT 55242467 AGCAA Start position changes from 55242467 to 55242468 is attributed to the presence of common bases A. Reference allele changes from AATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases A. Variant allele changes from AGCAA to GCAA is attributed to the presence of common bases A. SUCCESS diff --git a/test/data/minimal_example.out.uniprot.txt b/test/data/minimal_example.out.uniprot.txt index 6d114d38..0f0198aa 100644 --- a/test/data/minimal_example.out.uniprot.txt +++ b/test/data/minimal_example.out.uniprot.txt @@ -1,6 +1,6 @@ #genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status -PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS -EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS -EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number genomic_location_explanation Annotation_Status +PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS +EGFR 1956 GRCh37 7 55220240 55220240 + splice_region_variant,synonymous_variant Splice_Region SNP G T T ENST00000275493.2:c.630G>T p.X210_splice ENST00000275493 NM_005228.3 210 ctG/ctT 6/28 SUCCESS +EGFR 1956 GRCh37 7 55242468 55242486 + protein_altering_variant In_Frame_Del DEL ATTAAGAGAAGCAACATCT AGCAA GCAA ENST00000275493.2:c.2238_2256delinsGCAA p.Leu747_Ser752delinsGln p.L747_S752delinsQ ENST00000275493 NM_005228.3 746 gaATTAAGAGAAGCAACATCT/gaGCAA 19/28 Start position changes from 55242467 to 55242468 is attributed to the presence of common bases A. Reference allele changes from AATTAAGAGAAGCAACATCT to ATTAAGAGAAGCAACATCT is attributed to the presence of common bases A. Variant allele changes from AGCAA to GCAA is attributed to the presence of common bases A. SUCCESS diff --git a/test/data/my_variant_info_corner_cases.out.uniprot.txt b/test/data/my_variant_info_corner_cases.out.uniprot.txt index 336c3387..f26d5696 100644 --- a/test/data/my_variant_info_corner_cases.out.uniprot.txt +++ b/test/data/my_variant_info_corner_cases.out.uniprot.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF Annotation_Status -BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 0.0288928 0.0431947 0.0336575 0.012004 0.0438969 0.00355757 0.0178879 0.0324421 0.0705371 SUCCESS +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF genomic_location_explanation Annotation_Status +BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 0.0288928 0.0431947 0.0336575 0.012004 0.0438969 0.00355757 0.0178879 0.0324421 0.0705371 SUCCESS