[ensembl-dev] Change in SIFT and PolyPhen score

Wallace Ko myko at l3-bioinfo.com
Fri Dec 28 11:12:38 GMT 2018


Hello,

For the variant chr19:g.39075695C>T, the SIFT and PolyPhen score are
changed in recent versions of VEP.

VEP HGVSc SIFT PolyPhen
87 NM_000540.2:c.14759C>T - unknown(0)
88 NM_000540.2:c.14759C>T deleterious(0) unknown(0)
89 NM_000540.2:c.14759C>T deleterious(0) unknown(0)
90 NM_000540.2:c.14759C>T deleterious(0) probably_damaging(0.998)

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.

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.

Thank you.

Regards,
Wallace Ko
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20181228/34748a62/attachment.html>


More information about the Dev mailing list