We identified three clinical prognostic-related editing sites, which can also provide predictive values in HBV-/HCV-infected patients and non-alcoholic fatty liver disease patients, including editing sites in ALDH2 (chr12:111811793, A-to-I RNA editing), CNTNAP3B (chr9:41929326, C-to-T RNA editing), and CBWD5 (chr9:65675990, T-to-G RNA editing), of which ALDH2 is an HCC-related editing gene with high frequency (six HCC loss editing sites locates on the ALDH2 gene region). This evidence concerns the gene CNTNAP3B and hepatocellular carcinoma.