Missing gnomAD values for particular variant

[thomasyu888]

This particular variant can be found at: https://gnomad.broadinstitute.org/variant/1-144859816-TGGA-T?dataset=gnomad_r2_1 which has gnomAD values but processed.txt doesnt seem to show these gnomAD values.

• input.txt (Center input maf)
• processed.txt (Genome Nexus/annotation tools final output)

[leexgh]

@thomasyu888 Could you please post your application.properties here so we can better investigate? One thing might be worth mentioning is my_variant_info is required in genomenexus.enrichment_fields if you would like to get gnomAD data (e.g. genomenexus.enrichment_fields=annotation_summary,my_variant_info).

[thomasyu888]

@leexgh , here is my application.properties:

spring.batch.job.enabled=false
spring.jmx.enabled=false
chunk=100
genomenexus.enrichment_fields=annotation_summary,sift,polyphen,my_variant_info
genomenexus.isoform_query_parameter=isoformOverrideSource
genomenexus.base=https://genie.genomenexus.org/

The gnomAD values are being filled in for many variants, just seems to be missing for this one. I recall there was an issue like this before.

[thomasyu888]

Heres another variant that should be filtered out:

The variant is ITGA9 chr3 37778479 insG

https://genie-private.cbioportal.org/results/mutations?plots_horz_selection=%7B%7D&plots_vert_selection=%7B%7D&plots_coloring_selection=%7B%7D&tab_index=tab_visualize&Action=Submit&session_id=60e5cb9ee4b0f0abac8b9226

https://gnomad.broadinstitute.org/variant/3-37778478-A-AG?dataset=gnomad_r2_1