that aggregate the evidence for association across all functional variants in a biologically-equivalent unit (gene or pathway (4)). We expect to find a mix of functional and non-functional variants in most genes, but identifying which variants are likely to be functional has been challenging. Although prediction methods such as Polyphen2 (90) and SIFT (53) can predict that a variant might be functionally deleterious, these approaches are not completely accurate. Sensitivity and specificity may be low for subtle functional effects. A combined score might be more accurate than any single score (24, 64). Others have used frequency as a predictor of deleteriousness and either use thresholds so that only rare variants are considered (60) or use weights such that common variants are downweighted (56).
