Splicing Clinically Applicable Pathogenicity (S-CAP) Score

S-CAP is the first pathogenicity classifier designed to predict the pathogenicity of splice affecting rare single nucleotide variants in patient genomes with the high sensitivity required in the clinic. S-CAP combines sequenced-based features, evolutionary conservation, and existing metrics including SPIDEX, CADD, and LINSIGHT. S-CAP is comprised of 6 separate models, each designed to predict the pathogenicity of rare single nucleotide variants in a different splicing region, as is described in our paper. Further details can be found in our paper.

Splicing Region High sensitivity threshold
3' Intronic ≥ 0.006
3' Core Dominant ≥ 0.033
3' Core Recessive ≥ 0.264
Exonic ≥ 0.009
5' Core Dominant ≥ 0.034
5' Core Recessive ≥ 0.367
5' Extended ≥ 0.005
5' Intronic ≥ 0.006
S-CAP thresholds per splicing region

Download S-CAP scores

S-CAP source code

S-CAP public git repository can be found here.

How to cite

Jagadeesh, K., Paggi, J., Ye, J., Stenson, P., Cooper, D., Bernstein, J., and Bejerano, G. (2019). S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing. Nature Genetics, 2019. DOI: 10.1038/s41588-019-0348-4

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