[ensembl-dev] VEP HGVSp - Delins as substitutions in AA syntax

Bhavana Harsha bh4 at sanger.ac.uk
Wed Aug 2 10:20:14 BST 2017


Sorry to be back with what appears to be another bug in the Ensembl Variation API!
Not sure if you’re aware of this.

The hgvsp syntax for the CDS variant ‘ENST00000304494.5:c.330_331delGGinsAA’ as returned by VEP is

According to HGVS rules, the correct AA syntax should be ‘p.Trp110_Gly111delinsTer’ or ‘p.Trp110Ter’. (I’m not sure which is more appropriate here as they both seem correct)
A substitution of more than one AA should be reported as a delins.
See the 2nd question in the ‘Q&A’ section.

A simpler example is ‘ENST00000301067.7:c.258_259delGTinsTA’
VEP hgvsp = ‘ENSP00000301067.7:p.GluLeu86AspMet’
correct syntax = ‘ENSP00000301067.7:p.Glu86_Leu87delinsAspMet'

I think this is caused by the difference in the definition of the term ’substitution’ between Ensembl and HGVS.


Bhavana Harsha
Wellcome Trust Sanger Institute
Hinxton, UK
CB10 1SA

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