Documentation / Classification / Confidence Scores
Confidence Scores
What the Confidence Score Means
Each variant receives a continuous confidence score alongside its ACMG classification. The score reflects how far the variant's Bayesian point total is from the nearest classification boundary -- higher values indicate that the classification is well-supported by the available evidence.
Score Ranges
| Classification | Point Range | Confidence | Interpretation |
|---|---|---|---|
| Pathogenic | >= 10 | 0.80-0.99 | Higher points = higher confidence |
| Likely Pathogenic | 6-9 | 0.70-0.90 | Closer to 10 = higher confidence |
| VUS | 0-5 | 0.30-0.60 | Near boundaries = may reclassify with additional evidence |
| Likely Benign | -1 to -5 | 0.70-0.90 | Closer to -6 = higher confidence |
| Benign | <= -6 | 0.80-0.99 | Lower points = higher confidence |
How to Interpret
The confidence score is derived from the distance between the variant's point total and the nearest classification boundary. A Pathogenic variant with 15 points has higher confidence than one with exactly 10 points, because the 15-point variant would need more contradictory evidence to be reclassified.
VUS variants near the Likely Pathogenic boundary (5 points) are particularly important to note -- a single additional Supporting pathogenic criterion would reclassify them. These are high-priority candidates for additional evidence gathering (functional studies, family segregation, updated ClinVar review).
Important Note
The confidence score reflects classification evidence strength, not the probability of disease causation. A high-confidence Pathogenic classification means the evidence strongly supports pathogenicity under the ACMG framework, but clinical significance still depends on the patient's phenotype, inheritance pattern, and clinical context.