Some mutation annotations tend to exploit a single information type (e.g. phastCons or phyloP for conservation) and/or are restricted in scope (e.g. to missense changes). Thus, a broadly applicable metric that objectively weights and integrates diverse information is needed. Combined Annotation Dependent Depletion (CADD) is a framework that integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations.
CADD scores strongly correlate with allelic diversity, pathogenicity of both -coding and non-coding variants, and experimentally measured regulatory effects, +coding and non-coding variants, experimentally measured regulatory effects, and also highly rank causal variants within individual genome sequences. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS.
There are six subtracks of this track: four for every possible single nucleotide mutation, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover.
Single nucleotide variants (SNV): For SNVs, at every