We first compared the performance of PAFA, Eigen, CADD, GWAVA, FATHMM-MKL, and DANN on prioritizing coding variants from five well-studied genes (MLL2, CFTR, BRCA1, BRCA2, and TERT) associated with Kabuki syndrome, cystic fibrosis, breast cancer, or aggressive thyroid tumor, respectively. Here, CFTR is linked to breast cancer.