[ensembl-dev] Incorrect RefSeq HGVSc?

[Andrew Parton]

Hi,

Thanks for this report, it is an issue we are aware of. As you probably know, not all RefSeq transcripts completely match the reference genome. In cases where they don't, we are now using alignment files provided by NCBI to create a new reference, matching the transcript, and use this for consequence calling.

Our HGVS calculation does not currently use this reference modification, but it is something we are working on and aim to release later this year. VEP can report reference miss-matches for GRCh38, but these data are not available for GRCh37.

Kind Regards,
Andrew

> On 20 Jun 2018, at 10:53, Wallace Ko <myko at l3-bioinfo.com> wrote:
> 
> Hello,
> 
> I have a variant '2 31754395 . C T . . .' annotated by VEP web service: http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=5Xnr0Kx2ezfI8lj3-4292985 <http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=5Xnr0Kx2ezfI8lj3-4292985>
> 
> 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 <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.680G>A.
> 
> Checking VEP's HGVSc on Mutalyzer's name checker (https://mutalyzer.nl/name-checker?description=NM_000348.3%3Ac.679G%3EA <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.
> 
> Regards,
> Wallace Ko
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