Structural Variant Analysis Workflow

Systematic analysis of structural variants (deletions, duplications, inversions, translocations, complex rearrangements) for clinical genomics interpretation using ACMG-adapted criteria.

KEY PRINCIPLES:

1. Report-first approach - Create SV_analysis_report.md FIRST, then populate progressively
2. ACMG-style classification - Pathogenic/Likely Pathogenic/VUS/Likely Benign/Benign with explicit evidence
3. Evidence grading - Grade all findings by confidence level (★★★/★★☆/★☆☆)
4. Dosage sensitivity critical - Gene dosage effects drive SV pathogenicity
5. Breakpoint precision matters - Exact gene disruption vs dosage-only effects
6. Population context essential - gnomAD SVs for frequency assessment
7. English-first queries - Always use English terms in tool calls

Triggers