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Hereditary spherocytosis (HS) is a congenital hemolytic anemia that affects the cell membrane of red blood cells and is characterized by the presence of spherical-shaped erythrocytes in the peripheral blood film. The clinical manifestation of HS ranges from asymptomatic to severe cases that require transfusion during early childhood. HS is caused by mutations in red blood cell membrane protein encoding genes, including ANK1, EPB42, SLC4A1, SPTA1, and SPTB. Mutations of the ANK1 gene account for 75% of all HS cases, and these particular mutations are typically inherited in an autosomal dominant manner. In this study, heterozygous an ANK1 IVS3-2A>C mutation was identified in a 7-year-old girl with Coombs-negative and severe hemolytic jaundice using targeted next-generation sequencing (NGS) and Sanger sequencing. Spherocytes were observed in a peripheral smear. Osmotic fragility was increased, and glucose-6-phosphate dehydrogenase (G6PD) activity was normal. A genetic mutation screen for α- and β-thalassemia was negative. Autoimmune antibody tests were negative. Both the girl and her affected father received a splenectomy. Patient-derived peripheral blood mononuclear cells showed skipping of exon 4 in the mRNA, which confirmed the splicing mutation effect of the ANK1 IVS3-2A>C mutation. Moreover, the anemia was ameliorated after splenectomy. Our results demonstrate that the ANK1 IVS3-2A>C mutation may lead to exon 4 skipping of the ANK1 gene and cause HS.