Table 2 X-CAP prioritizes causal stopgains in patient exomes. Each row in the table describes a single patient, the causative gene and variant, the genotype of the variant, and the percentile-normalized score provided by each classifier. For each method, raw scores were percentile-normalized in comparison to the scores output by the classifier on the test set of \(\mathcal {D}_{\text {original}}\). All ten patients contain one rare stopgain and no other rare mutations in the causal gene. violetBolded entries have the highest percentile for a given variant. redItalicized entries would have been misclassified on the basis of the original authors’ recommendations (CADD, DANN, and Eigen do not provide a decision rule). X-CAP assigns the highest percentile six out of the ten times and mischaracterizes only one variant. No other tool assigns the highest percentile-normalized score more than once, and MutPred-LoF and ALoFT mischaracterize variants five and three times, respectively

From: X-CAP improves pathogenicity prediction of stopgain variants