[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
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