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<p>Hi Wallace,</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
ENST00000359596<br>
</p>
<p><br>
</p>
<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">
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<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">
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<div dir="ltr">Regards,
<div>Wallace Ko</div>
</div>
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