[ensembl-dev] Change in SIFT and PolyPhen score

[Sarah Hunt]

Hi Wallace,

Apologies for the partial response.

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.

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.

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.

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.

Best wishes,

Sarah


> 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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