Significantly, no enrichment of rare variants in <i>PNPLA3</i> or <i>TM6SF2</i> was observed across phenotypes.<h4>Conclusion</h4>In a cohort of children with histologically proven NAFLD, no genome-wide significant associations were found between rare genetic variation and advanced fibrosis or six other histologic features. Here, PNPLA3 is linked to metabolic dysfunction-associated steatotic liver disease.