Fig. 3

Density plot of the prediction probabilities for the 10,000 neutral 1KGP variant combinations used as a negative validation set. The X-axis represents the prediction probabilities, while the Y-axis shows the number of instances that were assigned the corresponding probability score. The plot visually presents the Disease-causing (green vertical line), \(99\%\) (orange vertical line) and \(99.9\%\) (red vertical line) confidence zones’ thresholds, indicating that 1% or less of all samples are to the right of the green line (i.e. were assigned a higher probability) and similarly 0.1% or less of all samples are to the right of the red line