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!
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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