Only Log AFP (OR = 0.46; 95% CI, 0.31–0.68, p = 0.0001), Log PIVKA-II (OR = 0.19; 95% CI, 0.12–0.29, p< 0.0001), Log CA199 (OR = 2.88; 95% CI, 1.95–4.26, p< 0.0001), Log CA125 (OR = 2.75; 95% CI, 1.5–5.01, p = 0.001), and HBV (OR = 0.13; 95% CI, 0.08–0.22, p< 0.0001) were the independent difference for the presence of ICC and HCC. This evidence concerns the gene MUC16 and intrahepatic cholangiocarcinoma.