[ensembl-dev] Change in SIFT and PolyPhen score

Sarah Hunt seh at ebi.ac.uk
Wed Jan 2 16:38:27 GMT 2019


Hi Wallace,

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


On 28/12/2018 11:12, Wallace Ko wrote:
> 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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