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Table 1 Working example of calculating the weighted Consensus score

From: Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting

Predictor

Prin1

 

Prin2

 

Prin3

 

PSAAP

0.56

 

0.25

 

0.25

 

MutPred

0.62

 

0.14

 

0.22

 

PMUT

0.46

 

0.36

 

-0.06

 

PolyPhen

-0.27

 

0.40

 

0.77

 

1-SIFT

0.06

 

0.79

 

-0.54

 

Varianta

PSAPPb

MutPredc

PMUTd

PolyPhene

SIFTf

 

Pathogenic

      

C609Y

0.85

0.90

0.98

0.97

0.00

 

Vector1 =

0.85 × 0.56

+0.90 × 0.62

+0.98 × 0.46

+0.97 × -0.27

+(1-0.00) × 0.06

= 1.283

Vector2 =

0.85 × 0.25

+0.90 × 0.14

+0.98 × 0.36

+0.97 × 0.40

+(1-0.00) × 0.79

= 1.869

Vector3 =

0.85 × 0.25

+0.90 × 0.22

+0.98 × -0.06

+0.97 × 0.77

+(1-0.00) × -0.54

= 0.559

     

Weighted sum (× 100)

= 371.1

Benign

      

V376A

0.07

0.13

0.19

0.04

0.60

 

Vector1 =

0.07 × 0.56

+0.13 × 0.62

+0.19 × 0.46

+0.04 × -0.27

+(1-0.60) × 0.06

= 0.220

Vector2 =

0.07 × 0.25

+0.13 × 0.14

+0.19 × 0.36

+0.04 × 0.40

+(1-0.60) × 0.79

= 0.436

Vector3 =

0.07 × 0.25

+0.13 × 0.22

+0.19 × -0.06

+0.04 × 0.77

+(1-0.60) × -0.54

= - 0.150

     

Weighted sum (× 100)

= 50.6

  1. aRET_HUMAN (UniProt #P07949) used as reference amino acid sequence. bPrimary Sequence Amino Acid Properties (PSAAP) algorithm, gene-specific trained. cAnalyzed with default settings at [57]. dAnalyzed with default settings at [58]. eAnalyzed with default settings at [59]. fAnalyzed with default settings at [60].