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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