Fig. 3

Model performance, evaluation, and analysis. a–c On-ss iSNVs. a Receiver operating characteristic curves (ROC) of RegSNPs-intron (solid green), SPANR (dotted blue), and CADD (dashed orange) on the validation set. b Selected probability cutoffs based on the false-positive rate (solid) and true-positive rate (dashed). The two dotted lines indicate FPR = 0.05 and 0.1, respectively. iSNVs with FPR < 0.05 are Damaging, those with 0.05 ≤ FPR < 0.1 are Possibly Damaging, and iSNVs with FPR ≥ 0.1 are Benign. c ROC of RegSNPs-intron (solid green) and SPANR (dotted blue) on the independent ClinVar test set. CADD was excluded since ClinVar was used in its model training. d–f Off-ss iSNVs, same as a–c