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<p>Hello,</p>
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<p>I'm working with PolyPhen2 scores and predictions in VEP 88 and comparing these back to scores reported in dbNSFP v3.0.</p>
<p>I find a large number of discrepancies between HumDiv scores from VEP and dbNSFP. I've looked at a small subset of 10 mismatches.</p>
<p>Directly comparing scores/predictions with PolyPhen2's website, all PolyPhen2 scores match with a dbNSFP score, and not a VEP score:</p>
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<div>CHROM POS REF ALT GENE VEP-FEATURE VEP-IMPACT VEP_CSQ VEP_POLYPHEN_SCORE VEP_POLYPHEN_PRED DBNSFP_POLYPHEN2_HDIV_SCORE DBNSFP_POLYPHEN2_HDIV_PRED pph2_prob pph2_FPR pph2_TPR<br>
2 73679572 C A ALMS1 NM_015120.4 MODERATE missense_variant 0.952 P 0.987,0.972,0.026 D,D,B 0.026 0.188 0.949<br>
1 216011417 A T USH2A NM_206933.2 MODERATE missense_variant 0.155 B 0.933 P 0.933 0.0573 0.804<br>
12 48398104 T C COL2A1 NM_001844.4 HIGH start_lost 0 U 0.219,0.14 B 0.14 0.136 0.923<br>
1 103427757 C G COL11A1 NM_080629.2 MODERATE missense_variant 0 U 0.999 D 0.999 0.00574 0.136<br>
12 48377197 G T COL2A1 NM_001844.4 MODERATE missense_variant 0.784 P 0.001,0.0 B 0 1 1<br>
6 70981396 C A COL9A1 NM_001851.4 MODERATE missense_variant 0.555 P 0.31,0.0 B 0.31 0.112 0.904<br>
10 73377145 G A CDH23 NM_001171930.1 MODERATE missense_variant 1 P 1.0,1.0,0.998 D 1 0.00026 0.00018<br>
1 216496954 T C USH2A NM_206933.2 MODERATE missense_variant 1 P 0.971,0.413 D,B 0.413 0.103 0.893<br>
17 18064707 C A MYO15A NM_016239.3 MODERATE missense_variant 0 U 0.941,0.761,0.165,0.523,0.981,0.953 P,P,B,P,D,P 0.523 0.0959 0.882<br>
1 103462662 C T COL11A1 NM_001190709.1 MODERATE missense_variant 1 P 1.0 D 1 0.00026 0.00018</div>
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<p>Any idea for this discrepancy?</p>
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<p>Thanks,</p>
<p>Brad<br>
</p>
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