The ISL1 (OD: 0.242, CI: 0.158–0.37, p-value: 0.158–0.37:), NFATc1 (OD: 2.53, CI: 1.64–3.89, p-value: 2.11 × 10–5), TBX5 (OD: 2.24, CI: 1.47–3.41, p-value:1.6 × 10–4) and MTHFR (OD: 10.46, CI: 5.68–19.26, p-value: 2.09 × 10–9:) variants were found to be in association with VSD in the Pakistani pediatric cohort whilst the VEGF (OD: 0.952, CI: 0.56–1.62, p-value: 0.8921) variants did not appear to be in association with the VSD (Table 3). Here, NFATC1 is linked to ventricular septal defect.