Ovotesticular Differences of Sexual Development (OTDSD) is a rare genetic variance defined by the coexistence of both testicular and ovarian tissues. Various molecular etiologies including SRY translocation or SOX9 pathogenic variants with different modes of inheritance have been associated with 46,XX intersex.  Here we describe a case of SRY-negative 46,XX OTDSD diagnosed after complex genetic analyses, including chromosomal microarray, DSD (Differences of Sexual Development) gene panel analysis, whole exome sequencing, and whole genome sequencing. Of these, only genome sequencing detected a pathogenic duplication in a non-coding region that contains the RevSex regulatory element, which modifies SOX9 expression and is associated with 46,XX DSD and complete sex reversal. This is the first clinical RevSex duplication detected by genome sequencing. We highlight the utility of whole genome sequencing in shortening the diagnostic odyssey and the importance of optimal counseling through a team-based multi-specialty approach for patients with DSDs.