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We report a case of an antenatal patient who was referred with an anomaly scan of a fetus suspected to have skeletal dysplasia associated with a hypoplastic heart. Genetic counselling was provided, and the opinions of the geneticist and paediatrician were sought. Risk and prognosis stratification were discussed with the couple. Amniocentesis was done as per the Preconception and Prenatal Diagnostic Techniques Act after informed consent. Termination of pregnancy was performed medically at 22 weeks and 2 days as per the Medical Termination of Pregnancy Amendment Act, 2021. On whole exome sequencing of the fetus, a genetic variant was detected, which confirmed a diagnosis of Ellis–van Creveld syndrome. Post-test genetic counselling was done to interpret the consequences of the variant(s), further genetic testing of parents (carriers) and extended carrier screening of family members. Infantogram and foetal echocardiography narrowed our differential diagnoses of skeletal dysplasia.