[ensembl-dev] Inconsistent RefSeq coding HGVS in VEP

[Wallace Ko]

Hello,

For the variant NC_000002.11:g.31754395C>T, VEP GRCh37 gives HGVSc of
NM_000348.3:c.679G>A
<http://grch37.rest.ensembl.org/vep/human/hgvs/NC_000002.11:g.31754395C%3ET?content-type=application/json&refseq=1&hgvs=1>
 (rs9332964).

By searching dbSNP, we can see that GRCh38 HGVS of rs9332964
is NC_000002.12:g.31529325C>T and VEP GRCh38 gives HGVSc of
NM_000348.3:c.680G>A
<http://rest.ensembl.org/vep/human/hgvs/NC_000002.12:g.31529325C%3ET?content-type=application/json&refseq=1&hgvs=1>
.

Searching ClinVar, NM_000348.3:c.680G>A gives result that correspond to
NC_000002.11:g.31754395C>T while NM_000348.3:c.679G>A doesn't.

Querying NM_000348.3:c.679G>A in Mutalyzer Name Checker
<https://mutalyzer.nl/name-checker?description=NM_000348.3%3Ac.679G%3EA>,
an error is shown that the reference base should be C instead of G. This
make me wonder if the HGVSc from VEP GRCH37 is incorrect.

Regards,
Wallace Ko
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