Synonymous Insertion before stop codon annotated as non silent insert

[joaoe]

Testcase, genome GRCm38 over transcript ENSMUST00000086738

##fileformat=VCFv4.1
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT
# Synonymous Insertion of an AA and new stop codon before the original stop codon:
# TTC ATC TGA -> TTC ATA TAA ATC TGA
chr1    100484695   .   C   CATATAA 5000    .   .   .

Varcode annotates this as

Insertion(variant=chr1 g.100484695_100484696insATATAA, transcript_id=ENSMUST00000086738, effect_description=p.1291insI)
* aa_mutation_start_offset=1291
* aa_mutation_end_offset=1292
* aa_ref=''
* aa_alt='I'

This should instead be a Silent() effect.

[joaoe]

In case you're wondering, the variant that showed this bug is in the cosmic VCF files (GRCh38).

14   38210558     C       CGCTCTGAGCCCGGGCCACGCAGGG

[joaoe]

Also, although this might seem far fetched, if the variant caller has a low gap penalty, it could choose to produce this kind of indel instead of a bunch of SNPs close by.