Resolving a Complex Neonatal Phenotype by Rapid Trio Whole‐Genome Sequencing: A De Novo 11q14.3–q22.3 Deletion and a Splicing‐Altering Synonymous <i>ANK1</i> Variant

BACKGROUND: Neonates with complex and evolving phenotypes often lack sufficiently specific clinical features to guide targeted genetic testing. Rapid trio whole-genome sequencing (WGS) may provide comprehensive etiologic clarification by simultaneously detecting sequence and structural variants. METHODS: Rapid trio WGS was performed in a preterm infant with dysmorphic features, cardiac anomalies, hemolytic anemia, and persistent intrahepatic cholestasis, together with her parents. A copy number variant was confirmed by chromosomal microarray analysis. The functional effect of a candidate single nucleotide variant was investigated using SpliceAI, reverse transcription PCR, agarose gel electrophoresis, and Sanger sequencing. RESULTS: The genetic diagnosis was achieved within 10 days. WGS identified a de novo heterozygous 15.6 Mb deletion at chromosome 11q14.3-q22.3, which was classified as pathogenic and accounted for the infant's congenital anomalies. A novel paternally inherited ANK1 synonymous variant, NM_000037.4:c.4104G>A was also identified, and its RNA analysis demonstrated exon 33 skipping, resulting in an in-frame deletion. Although the variant was classified as a variant of uncertain significance, its demonstrated splicing effect and the concordant spherocytosis phenotype in the infant and her father supported its clinical relevance. This integrated diagnosis informed surveillance, genetic counseling, and evaluation of the persistent cholestasis while avoiding further invasive investigation. CONCLUSION: Rapid trio WGS, complemented by functional RNA analysis, resolved distinct components of a complex neonatal phenotype by identifying both a pathogenic chromosomal deletion and a splicing-altering synonymous ANK1 variant. This case demonstrates the value of comprehensive genomic testing for precision diagnosis and individualized management in neonatal medicine.