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<p>Hi</p>
<p>The REST endpoint
(<a class="moz-txt-link-freetext" href="https://rest.ensembl.org/documentation/info/variation_consequence_types">https://rest.ensembl.org/documentation/info/variation_consequence_types</a>)
<br>
</p>
<p>and <br>
</p>
<p>the calculated consequences on (
<a class="moz-txt-link-freetext" href="https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html">https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html</a>)
should return the same values. <br>
</p>
<p>Thank you for for flagging the difference.<br>
<br>
The consequence SO:0001060 sequence_variant will be removed from
the REST endpoint in a future release.<br>
The consequence SO:0001628 intergenic_variant will be used
instead.</p>
<p>The three fields (SO_term, label, description) contain different
information on the consequence type and are used for different
purposes.<br>
<br>
SO_term - Sequence Ontology term for the consequence type<br>
label - A short description of the consequence type used in
labels<br>
description - A freetext description of the consequence type<br>
<br>
For example:<br>
SO_accession: SO:0001822<br>
SO_term: inframe_deletion<br>
description: An inframe non synonymous variant that deletes bases
from the coding sequence<br>
label: inframe deletion<br>
<br>
Regards<br>
Helen<br>
<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 27/12/2019 20:50, Ramiro Magno
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAFHVhtA+vYPhiTge30o+yYoGWpq3AyWa2avtZw9hB8U30Xhe_w@mail.gmail.com">
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<div dir="ltr">Hi Devs,<br>
<div><br>
</div>
<div>BTW: Still about the same endpoint, the output returns four
variables: SO_accession, SO_term, label and description. It
seems the actual values for the last three variables
(SO_term, label and description) always report the same
information. Is that right? Why so?</div>
<div><br>
</div>
<div>Cheers, RM</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, 27 Dec 2019 at 20:42,
Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com"
moz-do-not-send="true">ramiro.magno@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi Devs,<br>
<div><br>
</div>
<div>This endpoint: <a
href="https://rest.ensembl.org/documentation/info/variation_consequence_types"
target="_blank" moz-do-not-send="true">https://rest.ensembl.org/documentation/info/variation_consequence_types</a></div>
<div><br>
</div>
<div>returns one more consequence type than those listed
here: <a
href="https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html"
target="_blank" moz-do-not-send="true">https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html</a></div>
<div><br>
</div>
<div>The extra consequence type is the <i>sequence variant</i>
(SO:0001060).</div>
<div><br>
</div>
<div>Is this intended?</div>
<div><br>
</div>
<div>All the best,</div>
<div><br>
</div>
<div>Ramiro Magno</div>
</div>
</blockquote>
</div>
<br>
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