At multivariate logistic regression analysis including as independent variables noninvasive predictors of HCC (Model 1, middle panel), which can be applied even in NAFLD patients without histological evaluation of liver damage, HCC development was associated with older age (p < 0.001), male sex (p = 0.045), T2DM (p < 0.001), PNPLA3 I148M alleles (p = 0.010), TM6SF2 E167K alleles (p = 0.027), and remained strongly associated with MBOAT7 rs641738 alleles (OR 1.81, 95% c.i. 1.24–2.69; p = 0.002). Here, PNPLA3 is linked to metabolic dysfunction-associated steatotic liver disease.