Underreporting alteration by clinical sequencing: Integrative patho-genomic analysis captured /INI-1 deficiency in a vulvar yolk sac tumor.

•/INI1-deficient gynecologic tumors are rare and clinically aggressive. A subset shows primitive yolk sac tumor features.•Due to technical limitation of next generation sequencing (NGS) and interlaboratory variability in sequencing methodologies and analytical pipelines, deficiency caused by somatic copy number variations (SCNV) may be underreported by NGS.•To improve identification of /INI1-deficient neoplasm, we propose the following strategy: First, careful pathology slide review and detection of rhabdoid cells should raise the possibility of /INI1 deficiency. Second, INI1 IHC is a useful complementary test to exclude clinical suspicion of deficiency in the context of negative molecular reporting. Third, knowledge of potential underreporting of mutation would avoid underdiagnosis.