<div dir="ltr">Hi Guillermo,<br><br><div>For the ClinVar data Ensembl doesn't import the RefSeq reported, only the associated gene symbol. This along with other data are available in the attributes of the phenotype feature object ($pf->get_all_attributes).</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation<br><div><br></div><div><br><div class="gmail_extra"><div class="gmail_quote">On 17 June 2016 at 12:29, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
Dear devs,<br>
<br>
I've been using this plugin I made with the help of Will McLaren:
<a href="https://gist.github.com/guillermomarco/be0751f77b798d37ded14e5a884e4ff0" target="_blank">https://gist.github.com/guillermomarco/be0751f77b798d37ded14e5a884e4ff0</a><br>
I'm pretty happy with the results however I would like to improve
it. At this moment plugin outputs the selected phenotypes for all
the consequences per transcript. However this is not right.<br>
<br>
If I annotate the following record:<br>
<ul>
<li>chr11 128911444 . T C</li>
</ul>
<p>I get ClinVar information for all the transcripts consequences of
the variant. However If I'm not wrong I should only output ClinVar
for those consequences with same RefSeq as described by ClinVar,
in this case "NM_000890.3" associated to RCV000126421.3.<br>
</p>
<p>I don't understand exactly how does Ensembl handles Phenotype
information and if this kind of check is possible. The point
should be only output phentoypes not only based on variation but
check that transcript between phentoype and variation is the same.<br>
</p>
<p>Regards,<br>
Guillermo.<br>
</p>
</div>
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<br></blockquote></div><br></div></div></div></div>