In this study, we found that C allele rs2279026 of the TBC1D1 gene, G allele rs2279028 of the TBC1D1 gene, C allele rs780093 of the GCKR gene, and C allele rs1260326 of the GCKR gene were associated with a decreased risk of lean NAFLD in Chinese elderly population, T allele rs2206277 of the TFAP2B and C allele rs5215 of the KCNJ11 were combined with an increased risk of lean NAFLD. The gene discussed is TFAP2B; the disease is metabolic dysfunction-associated steatotic liver disease.