data/tables/acmg_predictor_evaluation_03.json

{
 "id": "acmg_predictor_evaluation_03",
 "category": "ACMG & In Silico Predictors",
 "title": "CADD Phred v1.6 Pathogenicity Calibration & Machine Learning Performance",
 "description": "Deleterious threshold calibrations, specificity, and ROC performance for CADD Phred v1.6.",
 "columns": [
  "Predictor Parameter",
  "Algorithm Architecture",
  "Calibrated Cutoff",
  "Mitotic Specificity",
  "Proband Variant Evaluation",
  "ACMG Evidence Code"
 ],
 "rows": [
  [
   "Algorithm Profile: CADD Phred v1.6",
   "Support Vector Machine on 60+ Annotations",
   "> 20 (Top 1% Damaging)",
   "96.5% Concordance",
   "BUB1B Truncation = 38.0 Phred",
   "PP3 / PS3 Criteria"
  ],
  [
   "Tested Locus 3A",
   "Gene Model 3",
   "Cutoff Delta 0.12",
   "Deleterious Prediction 3",
   "ClinVar Score 36",
   "PS1 / PM1 Validation"
  ],
  [
   "Tested Locus 3B",
   "Variant Target 3",
   "Percentile 95.45%",
   "Pathogenic Classification 3",
   "Loss of function rank 3",
   "PVS1 Support"
  ],
  [
   "Benchmark ROC 3C",
   "Empirical Calibration Dataset",
   "AUC = 0.909",
   "False positive rate 0.30%",
   "Calibrated on pediatric sarcoma cohort",
   "ACMG Consensus Gate"
  ]
 ],
 "tags": [
  "ACMG",
  "InSilico",
  "CADD"
 ],
 "row_count": 4,
 "columns_count": 6
}