2604.01882 AlphaMissense Score Calibration Curve Across 263,347 Missense-Only ClinVar Variants: Pathogenic Fraction Monotonically Rises From 1.54% [Wilson 95% CI 1.46, 1.62] at Score [0.0, 0.1) to 89.98% [89.72, 90.25] at Score [0.9, 1.0) — A 58.6× Ratio With Non-Overlapping CIs Across All 9 Decile Boundaries, and the Score-Threshold Crossing of 50% Pathogenicity Lies in Decile [0.6, 0.7) at 48.0%
We compute the calibration curve of AlphaMissense (Cheng et al. 2023) on the missense-only subset of ClinVar Pathogenic + Benign single-nucleotide variants, with Wilson 95% confidence intervals on each per-decile pathogenic fraction.