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<div>HI Bhavana,</div>
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<div>I think the transcript is on the -1 strand so the start/end coordinates have to be swapped.</div>
<div><a href="http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.783_661+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1">http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.783_661+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1</a></div>
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<div>But that's just a guess.</div>
<div>Best,</div>
<div>Daniel</div>
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<span style="font-weight:bold">From: </span><<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>> on behalf of Bhavana Harsha <<a href="mailto:bh4@sanger.ac.uk">bh4@sanger.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Friday, September 16, 2016 at 3:40 PM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>" <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>[ensembl-dev] VEP result does not match start-end coordinate and allele for hgvs syntax<br>
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Hello,
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<div class="">We’re trying to validate some mutations and see other co-located variants by using the VEP REST service for GRCh37, like this:</div>
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<div class=""><a href="http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1" class="">http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1</a></div>
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<div class="">And I get the following error:</div>
<div class="">{“error":"Start (52440390) must be less than or equal to end+1 (52440270)"}</div>
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<div class="">If I include the deleted sequence in the hgvs syntax, I get a different error:</div>
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<div class="">Input:</div>
<div class=""><a href="http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG?content-type=application/json;canonical=1&ccds=1&hgvs=1" class="">http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG?content-type=application/json;canonical=1&ccds=1&hgvs=1</a></div>
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<div class="">Output:</div>
<div class="">{“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)"}</div>
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<div class="">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.</div>
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<div class="">Is there something I’m missing here?</div>
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<div class="">Cheers,</div>
<div class="">Bhavana</div>
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---------------------------------------------<br class="">
Bhavana Harsha<br class="">
Bioinformatician<br class="">
COSMIC<br class="">
Wellcome Trust Sanger Institute<br class="">
Hinxton, UK<br class="">
CB10 1SA<br class="">
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