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AR stopgain/nonsense annotated as frameshift #665

Open a1618617 opened 2 years ago

a1618617 commented 2 years ago

Describe the bug Hey guys,

The following AR variant was annotated as a frameshift variant, however based on the c.HGVS and p.HGVS it should have been a deletion with a stop-gain molecular consequence. This is possibly a bug, unsure how many more are affected.

http://frgeneseq02.imvs.sa.gov.au:92/variantopedia/view_variant/55173790

image

davmlaw commented 2 years ago

I raised an issue about this over at VEP - I agree with you, so if you want to argue with them more go for it....

https://github.com/Ensembl/ensembl-vep/issues/1196

davmlaw commented 2 years ago

Thuong commented on the VEP issue.

FYI I have another issue - https://github.com/SACGF/variantgrid/issues/579 - which is to introduce a new annotation that records an early stop, and how far away it is. This will be separate from "molecular consequence" as that's just read straight from VEP

davmlaw commented 2 years ago

I have also run this through Annovar (not done yet but url should show it soon)

https://wannovar.wglab.org/done/376677/u_5EGvr2PkKcq6Ie/index.html

Had ExonicFunc=stopgain - commented on VEP issue