In the gene–gene interaction analysis, the MDR algorithm yielded three models; nevertheless, the model that showed the most consistent results was that formed by PNPLA3 (rs738409), GCKR (rs780094), and MBOAT7 (rs641738) with a CVC of 10/10 and a Testing accuracy of 0.6084 (p = 0.001), demonstrating an epistatic effect of these genes on HCC risk in the Mexican population. The gene discussed is MBOAT7; the disease is hepatocellular carcinoma.