ObjectiveThe balance between benefits and risks of discordant outcomes makes the Genome‐Wide Non‐Invasive Prenatal Test (GW‐NIPT) controversial. This study aims to evaluate performance and clinical utility in a wide cohort of unselected clinical cases from a single center when a standardized protocol is applied and integrated with a secondary algorithm for data interpretation.MethodIn 2 years, over 70,000 pregnant patients underwent GW‐NIPT for fetal common trisomies, sex chromosome aneuploidies, rare autosomal aneuploidies, segmental abnormalities (CNVs ≥ 7 Mb) and microdeletions (CNVs < 7 Mb). All samples were uniformly processed with Veriseq NIPT Solution v2 and analyzed using all data metrics along with a home‐made algorithm for sequencing data analysis. Results were retrospectively reviewed for clinical outcomes.ResultsAmong 71,883 eligible cases including twin pregnancies, 1011 (1.4%) received a positive result and 781 were confirmed by invasive prenatal diagnosis. Clinical sensitivity ranged from 99.65% for common trisomy (T21, T18, T13) to 83.33% for microdeletions, while specificity remained high (99.98%) for each class of fetal abnormalities detected.ConclusionsIntegrating a standardized protocol with an internal algorithm allowed discordant results to be reduced, yielding high accuracy. Observed reliability in detecting genome‐wide chromosomal conditions reinforced the expanded NIPT utility in clinical practice.