<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hi Emily,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">It’s the position on the RefSeq transcript (1043_1044) and the reading frame that are off by one. I got a clarification in a separate email that for this RefSeq transcript there is an insertion that’s not present in the reference. </div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Regards,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Vasisht</div> <div id="bloop_sign_1423061593695180800" class="bloop_sign"></div> <br><p style="color:#000;">On February 4, 2015 at 4:02:59 AM, Emily Perry (<a href="mailto:emily@ebi.ac.uk">emily@ebi.ac.uk</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div bgcolor="#FFFFFF" text="#000000"><div></div><div>
<title></title>
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">
<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>
<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>
<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>
_______________________________________________
<br>Dev mailing list Dev@ensembl.org
<br>Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
<br>Ensembl Blog: http://www.ensembl.info/
<br></div></div></span></blockquote></body></html>