The score assigned by Conseq was validated using PolyPhen (http://www.bork.embl-heidelberg.de/polyPhen/), which assigns scores, derived from likelihood matrices, as "benign", "possibly damaging", "probably damaging", or "unknown".
PolyPhen-2 categorizes the variants in three groups: benign, possibly damaging, and probably damaging.
For predictions by PolyPhen, SNPs were classified into three categories: benign, possibly damaging, and probably damaging.
It divides mutation into several categories such as benign, possibly damaging, or probably damaging on the basis of structure information and functional annotation.
PolyPhen categorizes the SNPs as benign, possibly damaging, or probably damaging on the basis of site-specific sequence conservation by estimating the position-specific independent count (PSIC) score for every variant and also calculates the score difference between variants [ 11].
The HVt group showed pulmonary oedema, worsening of the pulmonary histological consisting in benign vascular damage, and myocyte injury.
PolyPhen has outcomes of "benign", "possibly damaging" and "probably damaging".
The potential impact of each nonsynonymous change is reported as tolerated or not tolerated (SIFT), or benign, possibly damaging, or probably damaging (PolyPhen).
PolyPhen-2 [ 30] categorizes mutations as benign, possibly damaging, or probably damaging, based on pairs of false-positive rate (FPR) thresholds.
There are three qualitative measures available from PolyPhen: "benign", "possibly damaging protein", and "probably damaging protein".
