[ensembl-dev] VEP : Incorrect hgvsp syntax

[Bhavana Harsha]

Hello,

I seem to have mixed two separate examples in my email, sorry.
These are the correct ones:

Input : 3:g.41266031_41266626del
http://grch37.rest.ensembl.org/vep/human/hgvs/3:g.41266031_41266626del?content-type=application/json;xref_refseq=1&canonical=1&ccds=1&hgvs=1<http://grch37.rest.ensembl.org/vep/human/hgvs/3:g.41266017_41266633del?content-type=application/json;xref_refseq=1&canonical=1&ccds=1&hgvs=1>
VEP returns   : ENSP00000344456.5:p.Leu10_Ter142delinsTyr
Correct result : ENSP00000344456.5:p.Leu10_Asn141del

Cheers,
Bhavana


On 25 Sep 2017, at 17:01, Bhavana Harsha <bh4 at sanger.ac.uk<mailto:bh4 at sanger.ac.uk>> wrote:

Hello,

When I run VEP (GRCh37) using the following input :
3:g.41266017_41266633del

I get ‘ENSP00000379486.3:p.Leu10_Ter142delinsTyr’

We think the protein change should be ‘p.Leu10_Asn141del’, as confirmed by Mutalyzer.

The ref peptide sequence returned does not correspond to the protein sequence in Ensembl for ‘ENSP00000379486.3’. (They start to deviate at position 80).

I ran VEP using the REST API as well as the web interface, for GRCh37.
http://grch37.rest.ensembl.org/vep/human/hgvs/3:g.41266031_41266626del?content-type=application/json;xref_refseq=1&canonical=1&ccds=1&hgvs=1


Is there something I’m doing wrong?


Regards,
Bhavana




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




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