[ensembl-dev] Incorrect RefSeq HGVSc?

Wallace Ko myko at l3-bioinfo.com
Wed Jun 20 10:53:10 BST 2018


I have a variant '2 31754395 . C T . . .' annotated by VEP web service:

The resulting HGVS notations are:

   - HGVSc: NM_000348.3:c.679G>A
   - HGVSp: NP_000339.2:p.Arg227Gln

Searching the HGVSp on ClinVar, a corresponding  result
https://www.ncbi.nlm.nih.gov/clinvar/variation/3351 is found. However, the
coding HGVS on ClinVar's web page is NM_000348.3:c.*680*G>A.

Checking VEP's HGVSc on Mutalyzer's name checker (
https://mutalyzer.nl/name-checker?description=NM_000348.3%3Ac.679G%3EA), an
error shows that the reference base at c.679 is C instead of G.

I wonder if the HGVSc given by VEP is correct. Thank you.

Wallace Ko
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