Table 1 Performance assessment of in silico prediction tools on experimentally validated variants (n = 257).

From: Blood RNA analysis can increase clinical diagnostic rate and resolve variants of uncertain significance

Scoring metric

n Missing

Sensitivity

Specificity

Accuracy

PPV

NPV

HSF (2%)

28

0.8941

0.3958

0.5808

0.4663

0.8636

SpliceAI (0.2)

11

0.8987

0.9162

0.9106

0.8353

0.9503

Alamut SSF (5%)

5

0.7317

0.9294

0.8651

0.8333

0.8778

Alamut MES (10%)

1

0.7381

0.9070

0.8516

0.7949

0.8764

Alamut NNSplice (5%)

11

0.6923

0.8631

0.8089

0.7013

0.8580

Alamut 2/3

14a

0.7237

0.9162

0.8560

0.7971

0.8793

  1. Values have been calculated omitting the missing scores for each tool.
  2. HSF Human Splicing Finder, MES MaxEntScan, NPV negative predictive value, PPV positive predictive value, SSF Splice Site Finder.
  3. a11 variants missing one score, three variants missing two scores.
Back to article page