<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<p><br>
</p>
<p>Hi Bhavana,</p>
<p>Thanks for reporting this one. It is fixed in release/89 and will
go live on our REST server later in the month.</p>
<p>Best wishes,</p>
<p>Sarah<br>
</p>
<br>
<div class="moz-cite-prefix">On 02/08/2017 10:20, Bhavana Harsha
wrote:<br>
</div>
<blockquote
cite="mid:9C3E14F0-F40B-4AB8-A2EB-88A10F4F4630@sanger.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hello,
<div class=""><br class="">
</div>
<div class="">Sorry to be back with what appears to be another bug
in the Ensembl Variation API!</div>
<div class="">Not sure if you’re aware of this.</div>
<div class=""><br class="">
</div>
<div class="">The hgvsp syntax for the CDS variant
‘ENST00000304494.5:c.330_331delGGinsAA’ as returned by VEP is</div>
<div class="">‘ENSP00000307101.5:p.TrpGly110TerSer’</div>
<div class=""><br class="">
</div>
<div class="">According to HGVS rules, the correct AA syntax
should be ‘p.Trp110_Gly111delinsTer’ or ‘p.Trp110Ter’. (I’m not
sure which is more appropriate here as they both seem correct)</div>
<div class="">A substitution of more than one AA should be
reported as a delins.</div>
<div class="">See the 2nd question in the ‘Q&A’ section.</div>
<div class=""><a moz-do-not-send="true"
href="http://varnomen.hgvs.org/recommendations/protein/variant/delins/"
class="">http://varnomen.hgvs.org/recommendations/protein/variant/delins/</a></div>
<div class=""><br class="">
</div>
<div class="">A simpler example is
‘ENST00000301067.7:c.258_259delGTinsTA’ </div>
<div class="">VEP hgvsp <span class="Apple-tab-span" style="white-space:pre"></span>= ‘ENSP00000301067.7:p.GluLeu86AspMet’</div>
<div class="">correct syntax <span class="Apple-tab-span" style="white-space:pre">
</span>= ‘ENSP00000301067.7:p.Glu86_Leu87delinsAspMet'</div>
<div class=""><br class="">
</div>
<div class="">I think this is caused by the difference in the
definition of the term ’substitution’ between Ensembl and HGVS.</div>
<div class=""><a moz-do-not-send="true"
href="https://www.ensembl.org/info/genome/variation/index.html"
class="">https://www.ensembl.org/info/genome/variation/index.html</a></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class="">Bhavana</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<br class="">
<div class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant: 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="color: rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant: 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="">
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>