Introduction Clinical Whole Exome Sequencing (WES) offers a high diagnostic yield test by detecting pathogenic variants in all coding genes of the human genome. WES is poised to consolidate multiple genetic tests by accurately identifying Copy Number Variation (CNV) events, typically necessitating microarray analyses. However, standard commercial exome kits are limited to targeting exon coding regions, leaving significant gaps in coverage between genes which could hinder comprehensive CNV detection. To replace microarrays, advances in both assay design and computation methods are needed. Methods Addressing the need for comprehensive coverage, Twist Bioscience has developed an enhanced Twist Exome 2.0 Plus Comprehensive Exome Spike-in capture panel with added backbone probes. These probes target common SNPs polymorphic in multiple populations and are evenly distributed in the intergenic and intronic regions, with three varying densities at 25kb, 50kb, and 100kb intervals. This backone enables the genome-wide detection of CNVs and loss of heterozygosity (LOH), on top of single nucleotide variations (SNVs) and small insertions and deletions (InDels) that come with Twist Exome 2.0 product offering. Concurrently, Golden Helix has developed a multi-modal CNV caller designed specifically for target-capture NGS data to detect single-exon to whole-chromosome aneuploid CNV events. This study evaluates the combined efficacy of the backbone-probe enhanced exome capture panel and VS-CNV 2.6 in identifying known CNVs using the Coriell CNVPANEL01 reference set of 43 samples. Results The integration of the enhanced capture panel with VS-CNV 2.6 achieved a 100% sensitivity rate for the detection of known CNV events at all three probe densities. The application of best-practice quality metrics and filters was shown to have a minimal impact on this high sensitivity. Furthermore, the inclusion of high-density backbone probes improves the resolution and precision of CNV event boundaries. Conclusion The findings underscore the potential of the augmented Twist Exome in tandem with the VS-CNV caller. This combination presents a promising alternative to conventional microarray assays, potentially obviating the need for additional testing in clinical CNV detection. The study's results advocate for the implementation of this integrated approach as a more efficient and equally sensitive method for CNV analysis in a clinical setting.