[ensembl-dev] HGVS shift in GRCh37 and GRCh38

[Bhavana Harsha]

Hello,

We’ve come across something strange in VEP.

For the GRCh37 variant 17:g.16029315_16029421del, VEP returns the following transcript annotation:
HGVSg: 17:g.16029316_16029422del
HGVSc: ENST00000395851.1:c.1609_1634+81del
HGVSc-offset = 0
HGVSg-offset = 1

When we lift-over the genomic variant to GRCh38 (using the Ensembl API) and run VEP we get the following annotation for the same transcript:
Input: 17:g.16126002_16126108del
HGVSg: 17:g.16126003_16126109del
HGVSc: ENST00000395851.5:c.1609_1634+81del
HGVSc-offset = -1
HGVSg-offset = 1


Why does it shift the genomic syntax by 1 position in both the assemblies?
Shouldn’t GRCh37 VEP have shifted it by 2 bases or have I missed something here?

We’re on campus and I’m happy to meet to explain this further, if needed.



Regards,
Bhavana







---------------------------------------------
Bhavana Harsha
Senior Bioinformatician
COSMIC
Wellcome Trust Sanger Institute
Hinxton, UK
CB10 1SA




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20181128/410fabeb/attachment.html>