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<p>Hi Wallace,</p>
<p>Apologies for the partial response. <br>
</p>
<p>Prior to release 90, we did not calculate SIFT and PolyPhen2
scores for RefSeq transcripts, though they were available for
those with translations identical to an Ensembl transcript.
Although the GRCh37 transcript sets have been frozen for some
time, we update our GRCh37 variation data roughly annually, and
results from the analysis of new Ensembl GRCh38 translations would
be made available then. <br>
</p>
<p>The difference in SIFT results - the change from no data to a
prediction - will be due to results for a transcript matching
NM_000540.2 becoming available in release 88.</p>
<p>We re-ran our PolyPhen pipeline for e!90 when we noticed slightly
lower missingness rates after a change of hardware. We suspected
changes in the cluster set up led to less high-memory alignment
failures, but were not in a position to test this.</p>
<p>We now routinely calculate SIFT and PolyPhen2 scores for RefSeq
transcripts for our GRCh38 releases, which happen roughly
quarterly. Due to the scheduling of when RefSeq transcript data
becomes available in our release process, these scores are
available in VEP the release after the transcripts are available.<br>
</p>
<p>Best wishes,</p>
<p>Sarah<br>
</p>
<br>
<blockquote type="cite"
cite="mid:d57bc130-4172-5bd5-9f5e-1bdcacc0c520@ebi.ac.uk">
<div class="moz-cite-prefix">On 28/12/2018 11:12, Wallace Ko
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CA+DTqFc0m5xEX-fE6ODLKc0wL0HHwtsTt64dxxZw5rPaBY4sGA@mail.gmail.com">
<meta http-equiv="content-type" content="text/html;
charset=UTF-8">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">Hello,
<div><br>
</div>
<div>For the variant chr19:g.39075695C>T, the
SIFT and PolyPhen score are changed in recent
versions of VEP.</div>
<div><br>
</div>
<div>
<table dir="ltr"
style="table-layout:fixed;font-size:10pt;font-family:arial,sans,sans-serif;width:0px;border-collapse:collapse;border:none"
cellspacing="0" cellpadding="0" border="1">
<colgroup><col width="42"><col width="171"><col
width="100"><col width="167"></colgroup><tbody>
<tr style="height:21px">
<td style="border:1px solid

rgb(0,0,0);overflow:hidden;padding:2px

3px;vertical-align:bottom">VEP</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(0,0,0)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">HGVSc</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(0,0,0)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">SIFT</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(0,0,0)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">PolyPhen</td>
</tr>
<tr style="height:21px">
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0)

rgb(0,0,0);overflow:hidden;padding:2px

3px;vertical-align:bottom;text-align:right">87</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">NM_000540.2:c.14759C>T</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">-</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">unknown(0)</td>
</tr>
<tr style="height:21px">
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0)

rgb(0,0,0);overflow:hidden;padding:2px

3px;vertical-align:bottom;text-align:right">88</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">NM_000540.2:c.14759C>T</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">deleterious(0)</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">unknown(0)</td>
</tr>
<tr style="height:21px">
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0)

rgb(0,0,0);overflow:hidden;padding:2px

3px;vertical-align:bottom;text-align:right">89</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">NM_000540.2:c.14759C>T</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">deleterious(0)</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">unknown(0)</td>
</tr>
<tr style="height:21px">
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0)

rgb(0,0,0);overflow:hidden;padding:2px

3px;vertical-align:bottom;text-align:right">90</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">NM_000540.2:c.14759C>T</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">deleterious(0)</td>
<td
style="border-width:1px;border-style:solid;border-color:rgb(204,204,204)

rgb(0,0,0) rgb(0,0,0)

rgb(204,204,204);overflow:hidden;padding:2px

3px;vertical-align:bottom">probably_damaging(0.998)</td>
</tr>
</tbody>
</table>
</div>
<div><br>
</div>
<div>The above table shows that
for NM_000540.2:c.14759C>T, SIFT is changed
from '-' to 'deleterious(0)' since VEP 88 and
PolyPhen is changed from 'unknown(0)' to
'probably_damaging(0.998)' since VEP 90.</div>
<div><br>
</div>
<div>There is no change in software version of
SIFT (sift5.2.2) and PolyPhen (2.2.2) in these
versions of VEP, so I wonder what causes to
the change in the prediction scores.</div>
<div><br>
</div>
<div>Thank you.</div>
<div><br clear="all">
<div>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">Regards,
<div>Wallace Ko</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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