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Klippel-Trénaunay Syndrome (KTS) is a genetic vascular malformation involving the capillary, lymphatic, and venous channels. Prenatal sonographic diagnosis of KTS with an enlarged fetal limb is well-known; however, postnatal gynecologic manifestations are rarely reported. KTS can cause clitoromegaly, vulvovaginal hemangioma, and heavy menstrual bleeding. Somatic mosaicism of the <i>PIK3CA</i> gene is considered as responsible for KTS but reports based on whole-genome sequencing are limited. A 31-year-old woman with KTS presented with bulging of the clitoris and vagina. Analysis of whole-genome sequencing variant data revealed that gene ontology terms related to development and differentiation such as ‘skeletal system morphogenesis’, ‘embryonic morphogenesis’, and ‘sensory organ development’ were nominally significant in non-coding regions. Variants in non-coding genes may be responsible for this phenotype.