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.
03-20-2019: S-CAP combined file with an interpretable sensitivity score for thresholding can be found here!
| 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 |
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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