data/tables/acmg_fathmm_xf_coding_noncoding.json

{
 "id": "acmg_fathmm_xf_coding_noncoding",
 "category": "ACMG & In Silico Predictors",
 "title": "FATHMM-XF High-Precision Coding & Non-Coding Pathogenicity",
 "description": "Machine learning kernel scoring functional consequences in human disease loci.",
 "columns": [
  "Target Locus",
  "Genomic Variant (GRCh38)",
  "HGVSc Notation",
  "In Silico Prediction Score",
  "Percentile Decile",
  "ACMG Evidence Trigger",
  "Clinical Categorization"
 ],
 "rows": [
  [
   "BUB1B",
   "chr15:40,205,811",
   "c.1972C>T (p.Arg658Ter)",
   "Score = 0.995 / 38.0 Phred",
   "Top 0.1% Constraint",
   "PVS1 (Loss-of-Function)",
   "Pathogenic (MVA1 Hallmark)"
  ],
  [
   "TRIP13",
   "chr5:895,302",
   "c.1060G>A (p.Gly354Ser)",
   "Score = 0.882 / 28.4 Phred",
   "Top 1.5% Constraint",
   "PS3 / PM1 / PP3",
   "Pathogenic (Mosaic Driver)"
  ],
  [
   "CEP57",
   "chr11:96,158,214",
   "c.403C>T (p.Arg135Ter)",
   "Score = 0.988 / 36.0 Phred",
   "Top 0.2% Constraint",
   "PVS1 (Loss-of-Function)",
   "Pathogenic (MVA2 Hallmark)"
  ],
  [
   "MAD1L1",
   "chr7:1,842,504",
   "c.1852C>T (p.Arg618Trp)",
   "Score = 0.794 / 26.2 Phred",
   "Top 3.8% Constraint",
   "PM1 / PP3 (Moderate)",
   "Likely Pathogenic (CIN Modifier)"
  ],
  [
   "CEP192",
   "chr18:12,874,103",
   "c.1504G>A (p.Ala502Thr)",
   "Score = 0.741 / 24.1 Phred",
   "Top 5.9% Constraint",
   "PP3 (Supporting)",
   "Variant of Uncertain Significance"
  ],
  [
   "TP53",
   "chr17:7,675,088",
   "c.524G>A (p.Arg175His)",
   "Score = 0.962 / 32.0 Phred",
   "Top 0.3% Constraint",
   "PS1 / PS3 / PP3",
   "Pathogenic (Somatic Sarcoma Hit)"
  ]
 ],
 "tags": [
  "ACMG",
  "InSilico",
  "fathmm_xf_coding_noncoding"
 ],
 "row_count": 6,
 "columns_count": 7
}