Spectrum of Copy Number Variants in Fetal Congenital Heart Disease and Their Clinical Implications: A Retrospective Study from a Tertiary Care Center

<b>Background/Objectives:</b> This study assesses the genetic basis of fetal congenital heart disease (CHD), which exhibits a complex etiology, by using chromosomal microarray analysis (CMA); it also elucidates perinatal outcomes and postnatal development to support prenatal diagnosis and genetic counseling. <b>Methods:</b> Pregnant women (n = 1195) who were diagnosed with fetal CHD based on echocardiography were selected along with those having an interventional prenatal diagnosis, all of whom underwent CMA. Depending on the gestational age, amniotic fluid or umbilical cord blood samples were collected. Patients were included if they were diagnosed with fetal CHD based on echocardiography. Those who could not consent to amniocentesis or umbilical vein puncture or who had contraindications for amniocentesis or umbilical vein puncture were excluded. Patients were studied until May 2025. <b>Results:</b> Of the 1195 fetuses with CHD, 140 had pathogenic copy number variation (pCNV). The pCNV detection rate in cases with a single CHD was 3.17%, whereas it was 13.51% in the group with multiple CHDs. The detection rate for pCNVs in patients with extracardiac abnormalities was 28.62%. The fetal and postnatal mortality rates were highest for fetuses with multiple CHDs. The survival rate was highest for fetuses with a single CHD. Early detection of CHD and timely genetic testing can inform clinical management of CHD-affected pregnancies; however, larger prospective studies are needed to establish their impact on perinatal outcomes. <b>Conclusions</b>: CMA provides valuable information for genetic counselling, as it identifies pathogenic variants associated with CHD. However, prognostic predictions should consider multiple clinical factors.