Prediction scores for the disease associated variants. Disease associated variants were annotated by GWAVA (A, B, C), Mutation Assessor (D), CADD (E) and GERP (F). GWAVA score noncoding variants. Mutation Assessor score coding variants. CADD score coding or noncoding variants. GERP estimates the evolutionary constraints on genomic site. There are there types of GWAVA score: Region Score (A), TSS Score (B) and Unmatched Score (C). GWAVA annotation results indicate that the functionality of noncoding disease variants degrade in the order of cancer predisposing germline variants, Mendelian disease variants, recurrent cancer somatic mutations and complex disease variants. (D) Mutation Assessor annotation result shows that more cancer predisposing germline variants, Mendelian disease variants and recurrent cancer somatic mutations are with at least medium functionality compared to complex disease variants. (E) CADD annotation result suggests that deleteriousness of disease variants essentially decrease in the order of Mendelian disease variants, cancer predisposing germline variants, recurrent cancer somatic mutations and complex disease variants. (F) GERP annotation result indicates that the evolutionary constraints on disease variants are positively correlated with the functionality of disease variants, namely, the greater the functionality of disease variants, the greater the evolutionary constraints.