CNVision: a computational framework for functional interpretation of intragenic copy number variants

CNVision, a containerized framework for intragenic CNVs, produced concordant reading-frame and coding-sequence predictions across 200 curated variants and resolved 15 previously discrepant classifications.

• Why it matters: Intragenic exon-level deletions and duplications are hard to interpret because breakpoint-to-exon, coding-boundary, orientation, and reading-frame relationships are inconsistently handled.
• What they did: CNVision ingests exon-based entries, genomic coordinates, and HGVS genomic notation, unifies them internally, maps to coding regions, computes affected coding sequence length at base-pair resolution, and classifies reading-frame consequences.
• The result: In 131 reported CNVs, 15 classifications differed from published interpretations, and independent UCSC Genome Browser manual analysis supported CNVision in all 15; runtime tests on 18 CNVs showed both geneticists were faster with CNVision.

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