This study examined the prevalence of medical diagnoses in youth with sex chromosome aneuploidy (SCA) compared to matched controls in a large pediatric health learning system (PEDSnet). There was a significantly higher relative risk of having diagnoses within the Cardiovascular, Endocrine, Mental Health, and Nervous systems for all SCAs compared to their matched controls, and within the Genitourinary system for Klinefelter syndrome specifically. The prevalence of SCAs (per 100,000 persons in PEDSnet) in the last decade was significantly lower than known birth prevalence for all SCA conditions, confirming under-ascertainment of these conditions. The age of first visit with an SCA diagnosis code declined after commercialization of non-invasive prenatal screening, with many more individuals being identified before one year of age (presumably due to prenatal identification). Finally, we validated that a diagnosis of Turner syndrome in PEDSnet was >90% accurate for identifying patients who truly have the condition.
