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Table 1 Pathogenicity scores for SNVs and their reported ranges in the dbsnfp database

From: GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data

Metric

Type

Implementation

Actual range

Imposed range for transformation

CADD

Composite

Score

-∞ to +∞

−7.53 to 35.79

DANN

Composite

Score

0 to 1

–

FATHMMa

Functionality

1-Score

-∞ to +∞

−16.13 to 10.64

fathmm-MKL

Composite

Score

0 to 1

–

GERP++_RS

Conservation

Score

-∞ to +∞

−12.3 to 6.17

M-CAP

Composite

Score

0 to 1

–

MetaLR

Composite

Score

0 to 1

–

MetaSVM

Composite

Score

-∞ to +∞

−2 to 3

MutationTastera

Functionality

1-Score if N/P; Score if A/D

0 to 1

–

phastCons

Conservation

Score

0 to 1

–

phyloP

Conservation

Score

-∞ to +∞

−13.28 to 1.2

Polyphen2_HDIV

Functionality

Score

0 to 1

–

Polyphen2_HVAR

Functionality

Score

0 to 1

–

PROVEANa

Functionality

1-Score

−14 to 14

–

SIFTa

Functionality

1-Score

0 to 1

–

VEST3

Functionality

Score

0 to 1

–

  1. aIn order to maintain uniform directionality, the complement (1 – score) of a value was taken so that across scores, a value of 0 consistently indicated benign variation and a value of 1 inferred maximal pathogenicity