[ensembl-dev] VEP result does not match start-end coordinate and allele for hgvs syntax

[Daniel Suveges]

HI Bhavana,

I think the transcript is on the -1 strand so the start/end coordinates have to be swapped.
http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.783_661+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1

But that's just a guess.
Best,
Daniel

From: <dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org>> on behalf of Bhavana Harsha <bh4 at sanger.ac.uk<mailto:bh4 at sanger.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Friday, September 16, 2016 at 3:40 PM
To: "dev at ensembl.org<mailto:dev at ensembl.org>" <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: [ensembl-dev] VEP result does not match start-end coordinate and allele for hgvs syntax

Hello,

We’re trying to validate some mutations and see other co-located variants by using the VEP REST service for GRCh37, like this:

http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1

And I get the following error:
{“error":"Start (52440390) must be less than or equal to end+1 (52440270)"}


If I include the deleted sequence in the hgvs syntax, I get a different error:

Input:
http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG?content-type=application/json;canonical=1&ccds=1&hgvs=1

Output:
{“error":"Reference allele extracted from ENST00000460680:52440390-52440269 (AGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAG) does not match reference allele given by HGVS notation ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG (GAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG)"}


This is strange because shouldn’t the transcript coordinates ‘ENST00000460680.1:c.661-783+1’ correspond to ‘3:g.52440268-52440391’? But these aren’t the coordinates returned and the allele sequence is inconsistent with the input.

Is there something I’m missing here?

Cheers,
Bhavana


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



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