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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].