Table 2.
Comparison of ClassifyCNV calls to the results of manual annotation by ACMG/ClinGen.
| ACMG/ClinGen classification | ClassifyCNV classification | ClassifyCNV performance evaluation | |||
|---|---|---|---|---|---|
| Classification | Count | Classification | Count (percentage) | Sensitivity | Specificity |
| Pathogenic/likely pathogenic | 23 |
Pathogenic/likely pathogenic Uncertain significance |
14 (60.9%) 9 (39.1%) |
60.9% | 98.4% |
| Benign/likely benign | 8 |
Benign/likely benign Uncertain significance |
2 (25.0%) 6 (75.0%) |
25% | 100% |
| Uncertain significance | 53 |
Uncertain significance Pathogenic/likely pathogenic |
52 (98.1%) 1 (1.9%) |
98.1% | 51.6% |
| Conflicting results | 30 |
Uncertain significance Pathogenic/likely pathogenic |
28 (93.3%) 2 (6.7%) |
- | - |
For 81% of CNVs, the ClassifyCNV result matched the ACMG/ClinGen result category. ClassifyCNV showed a high degree of specificity for pathogenic/likely pathogenic and benign/likely benign variants.