Among microRNAs, <i>miR-146a-5p</i> demonstrated the highest diagnostic accuracy for ventricular septal defects (VSDs), while panels of lncRNAs, such as <i>LINC00598</i>, <i>LINC01551</i>, and <i>GATA3-AS1</i>, exhibited high performance for atrial septal defects (ASDs). The gene discussed is GATA3; the disease is ventricular septal defect.