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Hi Vasisht<br>
<br>
I'm not entirely sure I understand your question. A CAG>C change
in the genome is equivalent to a CTG>G change or CT deletion in a
negative strand gene or transcript. What annotation is the VEP
giving you that you believe to be incorrect?<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 03/02/2015 23:27, Vasisht Tadigotla
wrote:<br>
</div>
<blockquote
cite="mid:etPan.54d15954.2463b9ea.133@Vasishts-MacBook-Pro"
type="cite">
<style>body{font-family:Helvetica,Arial;font-size:13px}</style>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica">Hi,</font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica"><br>
</font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica">I’m annotating a variant
using GRCh37 and the VEP in the v78 release and the HGVS
annotation of the refseq transcripts doesn’t seem to match up
to the sequences for those transcripts.</font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica"><br>
</font></div>
<div id="bloop_customfont" style="margin: 0px;"><font
face="Helvetica">The variant is in SLC37A4
(chr11:g.118895980CAG>C), the HGVS annotations
are NM_001467.5:c.1043_1044delCT
and NP_001458.1:p.Pro348ArgfsTer? and the amino acid is being
annotated as CCT/C. The aa change is the same for all refseq
transcripts in the annotation. </font></div>
<div id="bloop_customfont" style="margin: 0px;"><font
face="Helvetica"><br>
</font></div>
<div id="bloop_customfont" style="margin: 0px;"><font
face="Helvetica">The count seems to be off by one - it’s a
CTG/G change. The local sequence context is GCC CTG TTT with
the TG being deleted. </font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica"><br>
</font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica">The correct HGVS description
is NM_001467.5:c.1042_1043delCT and the protein is <span
style="color: rgb(51, 51, 51); line-height: 18px;">p.Leu348Valfs*53.
This is annotated correctly in the Ensembl transcripts - </span>ENST00000545985.1:c.1042_1043delCT, ENSP00000475241.1:p.Leu348ValfsTer53. </font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica"><br>
</font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica">The following options were used for
the annotation:</font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><font face="Helvetica"><br>
</font></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;">—offline —everything —merged </div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><br>
</div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;">The same issue exists with the web version of VEP:</div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><br>
</div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><a class="moz-txt-link-freetext" href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=Ba08mzoDSO2008gG-584627">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=Ba08mzoDSO2008gG-584627</a></div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><br>
</div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;"><br>
</div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;">Thanks,</div>
<div id="bloop_customfont" style="color: rgb(0, 0, 0); margin:
0px;">Vasisht</div>
<font face="Helvetica"><br>
</font>
<br>
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<br>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Officer
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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