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Hello -</div>
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We are running a local installation of VEP (v84) and are running it with –offline and –cache parameters. Caches were installed with the VEP script (we did not use custom caches - using <span style="font-family: Menlo; font-size: 11px;">homo_sapiens_merged/84_GRCh37</span>).
I have noticed in some cases the SIFT and Polyphen scores for transcripts are different than what is reported in dbNSFP3 for a variant. I was wondering what version of SIFT and Polyphen scores are included in the pre–built caches or if there are thoughts
on why they would be different. Additionally is it the polyphen v2 score or polyphen?</div>
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For example:</div>
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Missense variant 6:33143391:G>A has no SIFT scores available for any transcript from the VEP annotation. <font face="Calibri,sans-serif">From dbNSFP 3.1, the same variant has the following SIFT scores: 0.285;0.29;0.307 for the following transcripts: </font><font face="Calibri,sans-serif">ENST00000374708;ENST00000341947;ENST00000361917.</font></div>
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Thanks so much,</div>
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Ann </div>
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