The combination of AFP and serum EV-SF3B4 exhibited an AUC of 0.942 (95% CI:0.908–0.966) in the HCC vs. non-tumor model and an AUC of 0.935 (95% CI:0.899–0.962) in the HCC vs. CH/LC model. This evidence concerns the gene SF3B4 and hepatocellular carcinoma.