[ensembl-dev] Discrepancies between VEP and Condel, PPH2 and SIFT

[A. P. Levine]

I have noticed some discrepancies between the PolyPhen, SIFT and Condel scores as reported by the VEP compared with the scores reported by the three programs independently.

The variant I have been looking at is "chr7: 140501302 T/C" (build 37).

Using the VEP (either online or with the perl script):
PolyPhen	benign	0.382
Condel	neutral	0.418
SIFT	tolerated	0.09

Using the Condel server (http://bg.upf.edu/condel/analysis):
PPH2	0.6
Condel	0.673 	deleterious
SIFT	0.09

Using SIFT (http://sift.jcvi.org/www/SIFT_chr_coords_submit.html):
SNP Type	Nonsynonymous
Prediction	DAMAGING
SIFT Score	0.04
Median Information Content	2.93
Gene ID

And finally, using PolyPhen-2 with both HumDiv and HumVar classifier models (http://genetics.bwh.harvard.edu/pph2/bgi.shtml):
HumVar	possibly damaging	pph2_prob	0.791
HumDiv	possibly damaging	pph2_prob	0.942

What do you think might be happening here? Which versions of the various programs are being used by the VEP?

Thank you,

Adam

Adam P. Levine