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<p>Hi Bhavana,</p>
<p>Thanks for the clarification. This is an interesting example -
the long deletion spanning 2 exons and a full intron is not being
handled correctly. It won't be possible to update our REST or web
tools until our next release, but we will let you know when the
code is updated.</p>
<p>Best wishes,<br>
</p>
<p>Sarah<br>
</p>
<br>
<div class="moz-cite-prefix">On 26/09/2017 10:16, Bhavana Harsha
wrote:<br>
</div>
<blockquote
cite="mid:C3C53710-63C9-4EFA-A25C-B86AC5B22722@sanger.ac.uk"
type="cite">
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charset=windows-1252">
Hello,
<div class=""><br class="">
</div>
<div class="">I seem to have mixed two separate examples in my
email, sorry.</div>
<div class="">These are the correct ones:</div>
<div class=""><br class="">
</div>
<div class="">Input : 3:g.41266031_41266626del</div>
<div class=""><a moz-do-not-send="true"
href="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"
class="">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</a></div>
<div class="">VEP returns
: ENSP00000344456.5:p.Leu10_Ter142delinsTyr</div>
<div class="">Correct result : ENSP00000344456.5:p.Leu10_Asn141del</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Bhavana</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 25 Sep 2017, at 17:01, Bhavana Harsha <<a
moz-do-not-send="true" href="mailto:bh4@sanger.ac.uk"
class="">bh4@sanger.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space;" class="">
Hello,
<div class=""><br class="">
</div>
<div class="">When I run VEP (GRCh37) using the
following input :</div>
<div class="">3:g.41266017_41266633del</div>
<div class=""><br class="">
</div>
<div class="">I get
‘ENSP00000379486.3:p.Leu10_Ter142delinsTyr’</div>
<div class=""><br class="">
</div>
<div class="">We think the protein change should be
‘p.Leu10_Asn141del’, as confirmed by Mutalyzer.</div>
<div class=""><br class="">
</div>
<div class="">The ref peptide sequence returned does not
correspond to the protein sequence in Ensembl for
‘ENSP00000379486.3’. (They start to deviate at
position 80).</div>
<div class=""><br class="">
</div>
<div class="">I ran VEP using the REST API as well as
the web interface, for GRCh37.</div>
<div class=""><a moz-do-not-send="true"
href="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"
class="">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</a></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Is there something I’m doing wrong?</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Bhavana</div>
<div class=""><br class="">
</div>
<br class="">
<br class="">
<div class="">
<div style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant-ligatures: normal;
font-variant-position: normal; font-variant-caps:
normal; font-variant-numeric: normal;
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font-variant-east-asian: normal; font-weight:
normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;"
class="">
<br class="Apple-interchange-newline">
---------------------------------------------<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="">
</div>
<div style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant-ligatures: normal;
font-variant-position: normal; font-variant-caps:
normal; font-variant-numeric: normal;
font-variant-alternates: normal;
font-variant-east-asian: normal; font-weight:
normal; letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;"
class="">
<br class="">
</div>
<br class="Apple-interchange-newline">
</div>
<br class="">
</div>
</div>
</blockquote>
</div>
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