Synonimous FrameShift over stop codon not annotated as silent

[joaoe]

Testcase, using genome GRCm38, over transcript ENSMUST00000086738

##fileformat=VCFv4.1
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT

# The coding sequence at chr1/99772765 has transcript ID ENSMUST00000086738
# and the end looks like:
# TTC ATC TGA ACT ATT GTG TGG TCA TCT GGT CCT CTT TTT (...)
#         ^ stop codon

# Synonymous FrameShift over the stop codon: TGA -> TAG AAC ...
chr1    100484699   .   T   TA  5000    .   .   .

This is annotated as

StopLoss(variant=chr1 g.100484699_100484700insA, transcript_name=Cntnap5b-001, transcript_id=ENSMUST00000086738, effect_description=p.*1293 (stop-loss))
* aa_ref = "*"
* aa_alt = ""
* modifies_protein_sequence = True

I think this should be annotated as Silent(...)

[iskandr]

Thanks for submitting these @joaoe, I'll start looking through them tomorrow.

[iskandr]

Fixed by https://github.com/hammerlab/varcode/pull/173