Phenotypic spectrum and molecular characteristics of variants of uncertain significance in copy number variations associated with fetal cardiac malformations: a case series of 9 patients.

BACKGROUND

Copy number variants of uncertain significance (VUS-CNVs) pose significant challenges in prenatal counseling for congenital heart malformations (CHMs). Their clinical relevance remains poorly defined, particularly in the absence of postnatal validation.

OBJECTIVE

To characterize the phenotypic and molecular features of VUS-CNVs in CHM fetuses and evaluate their clinical implications.

METHODS

From a cohort of 644 fetuses with CHMs undergoing chromosomal microarray analysis (CMA), we identified 9 VUS-CNV cases. All reportable CNVs (≥200 kb or in known pathogenic regions such as 22q11.21) were validated by TaqMan qPCR. Detailed prenatal echocardiography, trio CMA (n = 7), and postnatal follow-up were integrated for comprehensive assessment.

RESULTS

VUS-CNVs were identified in 9 of 644 (1.40%) CMA-tested fetuses with CHMs. These included 3 in isolated CHM, 1 in complex CHM, 3 in CHM with extracardiac structural anomalies, and 2 in CHM with isolated soft markers. VUS-CNVs in non-isolated cases were larger (median: 2.5 Mb vs. 0.72 Mb in isolated CHM) and encompassed more OMIM-listed genes (mean: 3.8 vs. 1.5 in isolated CHM) than those in isolated CHM. Trio analysis reclassified 3 of 7 tested VUS-CNVs (2 as likely benign, 1 as likely pathogenic). Six pregnancies continued to term-3 with isolated and 3 with non-isolated CHM-and all live-born infants showed no major postnatal abnormalities. The three terminations involved non-isolated phenotypes; decisions were primarily driven by structural anomaly severity, though the VUS amplified prognostic uncertainty.

CONCLUSION

Although VUS-CNVs are uncommon in fetuses with CHMs, they occur more frequently in non-isolated phenotypes and carry the potential for future reclassification-posing significant challenges in prenatal genetic counseling. These two aspects underscore the necessity of trio-based genomic testing, cautious interpretation of results, and longitudinal follow-up. Given the limited sample size of this study, no causal relationship between VUS-CNVs and clinical phenotypes can be inferred; however, our findings support a risk-stratified management framework that integrates detailed fetal phenotyping, trio analysis, and postnatal follow-up to enable accurate variant interpretation and informed decision-making.