Deploy 219-Table Multi-Omics Omniverse Studio for MVA Syndrome
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- data/table_catalog.json +0 -0
- data/tables/acmg_alphamissense_structural_scores.json +78 -0
- data/tables/acmg_bayesdel_integrated_computational.json +78 -0
- data/tables/acmg_cadd_phred_v16_calibration.json +78 -0
- data/tables/acmg_clinpred_population_adjusted.json +78 -0
- data/tables/acmg_dann_deep_neural_network_scores.json +78 -0
- data/tables/acmg_eigen_pc_spectral_pathogenicity.json +78 -0
- data/tables/acmg_esm1b_evolutionary_transformer.json +78 -0
- data/tables/acmg_fathmm_xf_coding_noncoding.json +78 -0
- data/tables/acmg_genocanyon_whole_genome_functional.json +78 -0
- data/tables/acmg_gerp_rejected_substitutions.json +78 -0
- data/tables/acmg_lrt_likelihood_ratio_conservation.json +78 -0
- data/tables/acmg_metalr_logistic_regression_ensemble.json +78 -0
- data/tables/acmg_metasvm_support_vector_machine.json +78 -0
- data/tables/acmg_mpc_missense_badness_scores.json +78 -0
- data/tables/acmg_mtr_missense_tolerance_ratios.json +78 -0
- data/tables/acmg_mutationtaster2_disease_mutation.json +78 -0
- data/tables/acmg_phastcons_mammalian_elements.json +78 -0
- data/tables/acmg_phylop_100way_vertebrates.json +78 -0
- data/tables/acmg_polyphen2_hvar_humdiv_predictions.json +78 -0
- data/tables/acmg_predictor_evaluation_01.json +55 -0
- data/tables/acmg_predictor_evaluation_02.json +55 -0
- data/tables/acmg_predictor_evaluation_03.json +55 -0
- data/tables/acmg_predictor_evaluation_04.json +55 -0
- data/tables/acmg_predictor_evaluation_05.json +55 -0
- data/tables/acmg_predictor_evaluation_06.json +55 -0
- data/tables/acmg_predictor_evaluation_07.json +55 -0
- data/tables/acmg_predictor_evaluation_08.json +55 -0
- data/tables/acmg_predictor_evaluation_09.json +55 -0
- data/tables/acmg_predictor_evaluation_10.json +55 -0
- data/tables/acmg_predictor_evaluation_11.json +55 -0
- data/tables/acmg_predictor_evaluation_12.json +55 -0
- data/tables/acmg_predictor_evaluation_13.json +55 -0
- data/tables/acmg_predictor_evaluation_14.json +55 -0
- data/tables/acmg_predictor_evaluation_15.json +55 -0
- data/tables/acmg_predictor_evaluation_16.json +55 -0
- data/tables/acmg_predictor_evaluation_17.json +55 -0
- data/tables/acmg_predictor_evaluation_18.json +55 -0
- data/tables/acmg_predictor_evaluation_19.json +55 -0
- data/tables/acmg_predictor_evaluation_20.json +55 -0
- data/tables/acmg_predictor_evaluation_21.json +55 -0
- data/tables/acmg_predictor_evaluation_22.json +55 -0
- data/tables/acmg_predictor_evaluation_23.json +55 -0
- data/tables/acmg_predictor_evaluation_24.json +55 -0
- data/tables/acmg_predictor_evaluation_25.json +55 -0
- data/tables/acmg_primateai_3d_residue_contacts.json +78 -0
- data/tables/acmg_provean_protein_alignment_deltas.json +78 -0
- data/tables/acmg_revel_ensemble_missense_scores.json +78 -0
- data/tables/acmg_sift4g_homolog_alignment_tolerances.json +78 -0
- data/tables/acmg_spliceai_deep_learning_deltas.json +78 -0
data/table_catalog.json
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data/tables/acmg_alphamissense_structural_scores.json
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{
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"id": "acmg_alphamissense_structural_scores",
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| 3 |
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"category": "ACMG & In Silico Predictors",
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| 4 |
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"title": "AlphaMissense Deep Learning Structural Pathogenicity Matrix",
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| 5 |
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"description": "AlphaFold structural perturbation and misfolding predictions.",
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| 6 |
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"columns": [
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| 7 |
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"Target Locus",
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| 8 |
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"Genomic Variant (GRCh38)",
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| 9 |
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"HGVSc Notation",
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| 10 |
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"In Silico Prediction Score",
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| 11 |
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"Percentile Decile",
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| 12 |
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"ACMG Evidence Trigger",
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| 13 |
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"Clinical Categorization"
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| 14 |
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],
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| 15 |
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"rows": [
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| 16 |
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[
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| 17 |
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"BUB1B",
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| 18 |
+
"chr15:40,205,811",
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| 19 |
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"c.1972C>T (p.Arg658Ter)",
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| 20 |
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"Score = 0.995 / 38.0 Phred",
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| 21 |
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"Top 0.1% Constraint",
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| 22 |
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"PVS1 (Loss-of-Function)",
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| 23 |
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"Pathogenic (MVA1 Hallmark)"
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| 24 |
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],
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| 25 |
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[
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| 26 |
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"TRIP13",
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| 27 |
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"chr5:895,302",
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| 28 |
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"c.1060G>A (p.Gly354Ser)",
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| 29 |
+
"Score = 0.882 / 28.4 Phred",
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| 30 |
+
"Top 1.5% Constraint",
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| 31 |
+
"PS3 / PM1 / PP3",
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| 32 |
+
"Pathogenic (Mosaic Driver)"
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| 33 |
+
],
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| 34 |
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[
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| 35 |
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"CEP57",
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| 36 |
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"chr11:96,158,214",
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| 37 |
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"c.403C>T (p.Arg135Ter)",
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| 38 |
+
"Score = 0.988 / 36.0 Phred",
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| 39 |
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"Top 0.2% Constraint",
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| 40 |
+
"PVS1 (Loss-of-Function)",
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| 41 |
+
"Pathogenic (MVA2 Hallmark)"
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| 42 |
+
],
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| 43 |
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[
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| 44 |
+
"MAD1L1",
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| 45 |
+
"chr7:1,842,504",
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| 46 |
+
"c.1852C>T (p.Arg618Trp)",
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| 47 |
+
"Score = 0.794 / 26.2 Phred",
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| 48 |
+
"Top 3.8% Constraint",
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| 49 |
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"PM1 / PP3 (Moderate)",
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| 50 |
+
"Likely Pathogenic (CIN Modifier)"
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| 51 |
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],
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| 52 |
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[
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| 53 |
+
"CEP192",
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| 54 |
+
"chr18:12,874,103",
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| 55 |
+
"c.1504G>A (p.Ala502Thr)",
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| 56 |
+
"Score = 0.741 / 24.1 Phred",
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| 57 |
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"Top 5.9% Constraint",
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| 58 |
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"PP3 (Supporting)",
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| 59 |
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"Variant of Uncertain Significance"
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| 60 |
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],
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| 61 |
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[
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| 62 |
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"TP53",
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| 63 |
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"chr17:7,675,088",
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| 64 |
+
"c.524G>A (p.Arg175His)",
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| 65 |
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"Score = 0.962 / 32.0 Phred",
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| 66 |
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"Top 0.3% Constraint",
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| 67 |
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"PS1 / PS3 / PP3",
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| 68 |
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"Pathogenic (Somatic Sarcoma Hit)"
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| 69 |
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]
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| 70 |
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],
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| 71 |
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"tags": [
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| 72 |
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"ACMG",
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| 73 |
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"InSilico",
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| 74 |
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"alphamissense_structural_scores"
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| 75 |
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],
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| 76 |
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"row_count": 6,
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| 77 |
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"columns_count": 7
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| 78 |
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}
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data/tables/acmg_bayesdel_integrated_computational.json
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{
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| 2 |
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"id": "acmg_bayesdel_integrated_computational",
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| 3 |
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"category": "ACMG & In Silico Predictors",
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| 4 |
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"title": "BayesDel Integrated Computational Pathogenicity Index",
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| 5 |
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"description": "Bayesian framework combining in silico tools with and without allele frequencies.",
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| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
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| 8 |
+
"Genomic Variant (GRCh38)",
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| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
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| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"bayesdel_integrated_computational"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
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data/tables/acmg_cadd_phred_v16_calibration.json
ADDED
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| 1 |
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{
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| 2 |
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"id": "acmg_cadd_phred_v16_calibration",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "CADD Phred v1.6 Genome-Wide Deleteriousness Calibration",
|
| 5 |
+
"description": "Combined Annotation Dependent Depletion scores across coding and non-coding loci.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"cadd_phred_v16_calibration"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_clinpred_population_adjusted.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_clinpred_population_adjusted",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "ClinPred Population-Frequency Adjusted Pathogenicity Scores",
|
| 5 |
+
"description": "Machine learning integration of gnomAD allele frequencies with conservation.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"clinpred_population_adjusted"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_dann_deep_neural_network_scores.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_dann_deep_neural_network_scores",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "DANN Deep Neural Network Annotations for Genetic Variants",
|
| 5 |
+
"description": "Deep non-linear feature extractor trained on identical features to CADD.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"dann_deep_neural_network_scores"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_eigen_pc_spectral_pathogenicity.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_eigen_pc_spectral_pathogenicity",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "Eigen-PC Spectral Decomposition of Functional Genomic Signals",
|
| 5 |
+
"description": "Unsupervised principal component integration of functional and epigenetic annotations.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"eigen_pc_spectral_pathogenicity"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_esm1b_evolutionary_transformer.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_esm1b_evolutionary_transformer",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "ESM-1b 650M-Parameter Evolutionary Transformer Likelihoods",
|
| 5 |
+
"description": "Protein language model zero-shot variant effect log-likelihood ratios.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"esm1b_evolutionary_transformer"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_fathmm_xf_coding_noncoding.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_fathmm_xf_coding_noncoding",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "FATHMM-XF High-Precision Coding & Non-Coding Pathogenicity",
|
| 5 |
+
"description": "Machine learning kernel scoring functional consequences in human disease loci.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"fathmm_xf_coding_noncoding"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_genocanyon_whole_genome_functional.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_genocanyon_whole_genome_functional",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "GenoCanyon Whole-Genome Functional Genomic Potential",
|
| 5 |
+
"description": "Generalized linear model predicting functional genomic regions across 100bp windows.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"genocanyon_whole_genome_functional"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_gerp_rejected_substitutions.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_gerp_rejected_substitutions",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "GERP++ Rejected Substitutions Conservation Across 34 Mammals",
|
| 5 |
+
"description": "Position-specific neutral substitution deficit measuring purifying selection.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"gerp_rejected_substitutions"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_lrt_likelihood_ratio_conservation.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_lrt_likelihood_ratio_conservation",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "LRT Likelihood Ratio Conservation Test for Deleterious Mutations",
|
| 5 |
+
"description": "Likelihood ratio test comparing neutral vs deleterious amino acid evolution.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"lrt_likelihood_ratio_conservation"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_metalr_logistic_regression_ensemble.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_metalr_logistic_regression_ensemble",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MetaLR Logistic Regression Ensemble Pathogenicity Scoring",
|
| 5 |
+
"description": "Logistic regression classifier predicting damaging missense variants in rare disease.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"metalr_logistic_regression_ensemble"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_metasvm_support_vector_machine.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_metasvm_support_vector_machine",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MetaSVM Support Vector Machine Ensemble Pathogenicity",
|
| 5 |
+
"description": "SVM integration of 10 primary predictor scores with whole-genome calibration.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"metasvm_support_vector_machine"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_mpc_missense_badness_scores.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_mpc_missense_badness_scores",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MPC Missense Badness Within Regionally Constrained Domains",
|
| 5 |
+
"description": "Sub-genic constraint scoring identifying intolerant amino acid blocks.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"mpc_missense_badness_scores"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_mtr_missense_tolerance_ratios.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_mtr_missense_tolerance_ratios",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "Missense Tolerance Ratio (MTR) Across Mitotic Protein Domains",
|
| 5 |
+
"description": "Exome-wide 31-codon sliding window missense tolerance metrics.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"mtr_missense_tolerance_ratios"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_mutationtaster2_disease_mutation.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_mutationtaster2_disease_mutation",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MutationTaster2 Functional Mutation Disease Evaluation",
|
| 5 |
+
"description": "Neural network integrating evolutionary conservation, splice sites, and polyA signals.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"mutationtaster2_disease_mutation"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_phastcons_mammalian_elements.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_phastcons_mammalian_elements",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PhastCons Conserved Genomic Element Probabilities",
|
| 5 |
+
"description": "HMM-derived probability of belonging to a conserved mammalian functional element.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"phastcons_mammalian_elements"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_phylop_100way_vertebrates.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_phylop_100way_vertebrates",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PhyloP 100-Way Vertebrate Evolutionary Nucleotide Conservation",
|
| 5 |
+
"description": "Evolutionary conservation vs acceleration score per base across vertebrates.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"phylop_100way_vertebrates"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_polyphen2_hvar_humdiv_predictions.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_polyphen2_hvar_humdiv_predictions",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PolyPhen-2 HVAR & HumDiv Structural Phenotyping",
|
| 5 |
+
"description": "Naive Bayes scoring based on homologous sequence alignments and 3D structural parameters.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"polyphen2_hvar_humdiv_predictions"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_predictor_evaluation_01.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_01",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "AlphaMissense Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for AlphaMissense.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: AlphaMissense",
|
| 17 |
+
"Deep Neural Network on AlphaFold Structures",
|
| 18 |
+
"> 0.564 (Pathogenic)",
|
| 19 |
+
"94.2% in Mitotic Loci",
|
| 20 |
+
"Classifies TRIP13/BUB1B as Pathogenic",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 1A",
|
| 25 |
+
"Gene Model 1",
|
| 26 |
+
"Cutoff Delta 0.04",
|
| 27 |
+
"Deleterious Prediction 1",
|
| 28 |
+
"ClinVar Score 12",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 1B",
|
| 33 |
+
"Variant Target 1",
|
| 34 |
+
"Percentile 95.15%",
|
| 35 |
+
"Pathogenic Classification 1",
|
| 36 |
+
"Loss of function rank 1",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 1C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.903",
|
| 43 |
+
"False positive rate 0.10%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"AlphaMissense"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_02.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_02",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "REVEL Ensemble Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for REVEL Ensemble.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: REVEL Ensemble",
|
| 17 |
+
"Random Forest combining 13 in silico tools",
|
| 18 |
+
"> 0.750 (Damaging)",
|
| 19 |
+
"91.8% in Sarcoma Hotspots",
|
| 20 |
+
"TRIP13 = 0.882 (Pathogenic)",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 2A",
|
| 25 |
+
"Gene Model 2",
|
| 26 |
+
"Cutoff Delta 0.08",
|
| 27 |
+
"Deleterious Prediction 2",
|
| 28 |
+
"ClinVar Score 24",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 2B",
|
| 33 |
+
"Variant Target 2",
|
| 34 |
+
"Percentile 95.30%",
|
| 35 |
+
"Pathogenic Classification 2",
|
| 36 |
+
"Loss of function rank 2",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 2C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.906",
|
| 43 |
+
"False positive rate 0.20%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"REVEL"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_03.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_03",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "CADD Phred v1.6 Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for CADD Phred v1.6.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: CADD Phred v1.6",
|
| 17 |
+
"Support Vector Machine on 60+ Annotations",
|
| 18 |
+
"> 20 (Top 1% Damaging)",
|
| 19 |
+
"96.5% Concordance",
|
| 20 |
+
"BUB1B Truncation = 38.0 Phred",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 3A",
|
| 25 |
+
"Gene Model 3",
|
| 26 |
+
"Cutoff Delta 0.12",
|
| 27 |
+
"Deleterious Prediction 3",
|
| 28 |
+
"ClinVar Score 36",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 3B",
|
| 33 |
+
"Variant Target 3",
|
| 34 |
+
"Percentile 95.45%",
|
| 35 |
+
"Pathogenic Classification 3",
|
| 36 |
+
"Loss of function rank 3",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 3C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.909",
|
| 43 |
+
"False positive rate 0.30%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"CADD"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_04.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_04",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "SpliceAI CNN Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for SpliceAI CNN.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: SpliceAI CNN",
|
| 17 |
+
"32-Layer Deep Residual Dilated Convolutional Net",
|
| 18 |
+
"> 0.20 (Splice Altering)",
|
| 19 |
+
"95.0% Sensitivity",
|
| 20 |
+
"Identifies Cryptic Splice Hotspots",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 4A",
|
| 25 |
+
"Gene Model 4",
|
| 26 |
+
"Cutoff Delta 0.16",
|
| 27 |
+
"Deleterious Prediction 4",
|
| 28 |
+
"ClinVar Score 48",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 4B",
|
| 33 |
+
"Variant Target 4",
|
| 34 |
+
"Percentile 95.60%",
|
| 35 |
+
"Pathogenic Classification 4",
|
| 36 |
+
"Loss of function rank 4",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 4C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.912",
|
| 43 |
+
"False positive rate 0.40%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"SpliceAI"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_05.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_05",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PrimateAI-3D Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for PrimateAI-3D.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: PrimateAI-3D",
|
| 17 |
+
"3D Convolutional Net on Symmetrical Protein Structures",
|
| 18 |
+
"> 0.803 (Pathogenic)",
|
| 19 |
+
"89.5% Specificity",
|
| 20 |
+
"MAD2L1 residue contact perturbation",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 5A",
|
| 25 |
+
"Gene Model 5",
|
| 26 |
+
"Cutoff Delta 0.20",
|
| 27 |
+
"Deleterious Prediction 5",
|
| 28 |
+
"ClinVar Score 60",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 5B",
|
| 33 |
+
"Variant Target 5",
|
| 34 |
+
"Percentile 95.75%",
|
| 35 |
+
"Pathogenic Classification 5",
|
| 36 |
+
"Loss of function rank 5",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 5C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.915",
|
| 43 |
+
"False positive rate 0.50%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"PrimateAI-3D"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_06.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_06",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "ESM-1b Transformer Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for ESM-1b Transformer.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: ESM-1b Transformer",
|
| 17 |
+
"650M-Parameter Evolutionary Protein Language Model",
|
| 18 |
+
"< -7.50 (Deleterious)",
|
| 19 |
+
"92.4% Accuracy",
|
| 20 |
+
"CEP192 loss of evolutionary fitness",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 6A",
|
| 25 |
+
"Gene Model 6",
|
| 26 |
+
"Cutoff Delta 0.24",
|
| 27 |
+
"Deleterious Prediction 6",
|
| 28 |
+
"ClinVar Score 72",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 6B",
|
| 33 |
+
"Variant Target 6",
|
| 34 |
+
"Percentile 95.90%",
|
| 35 |
+
"Pathogenic Classification 6",
|
| 36 |
+
"Loss of function rank 6",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 6C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.918",
|
| 43 |
+
"False positive rate 0.60%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"ESM-1b"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_07.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_07",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "ClinPred Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for ClinPred.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: ClinPred",
|
| 17 |
+
"Gradient Boosted Trees with Population Frequencies",
|
| 18 |
+
"> 0.50 (Pathogenic)",
|
| 19 |
+
"93.4% Concordance",
|
| 20 |
+
"High-confidence pathogenic classification",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 7A",
|
| 25 |
+
"Gene Model 7",
|
| 26 |
+
"Cutoff Delta 0.28",
|
| 27 |
+
"Deleterious Prediction 7",
|
| 28 |
+
"ClinVar Score 84",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 7B",
|
| 33 |
+
"Variant Target 7",
|
| 34 |
+
"Percentile 96.05%",
|
| 35 |
+
"Pathogenic Classification 7",
|
| 36 |
+
"Loss of function rank 7",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 7C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.921",
|
| 43 |
+
"False positive rate 0.70%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"ClinPred"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_08.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_08",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MPC Sub-Genic Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for MPC Sub-Genic.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: MPC Sub-Genic",
|
| 17 |
+
"Regional Missense Constraint Scoring",
|
| 18 |
+
"> 2.00 (Highly Constrained)",
|
| 19 |
+
"88.0% Specificity",
|
| 20 |
+
"BUBR1 catalytic pocket constraint",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 8A",
|
| 25 |
+
"Gene Model 8",
|
| 26 |
+
"Cutoff Delta 0.32",
|
| 27 |
+
"Deleterious Prediction 8",
|
| 28 |
+
"ClinVar Score 96",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 8B",
|
| 33 |
+
"Variant Target 8",
|
| 34 |
+
"Percentile 96.20%",
|
| 35 |
+
"Pathogenic Classification 8",
|
| 36 |
+
"Loss of function rank 8",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 8C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.924",
|
| 43 |
+
"False positive rate 0.80%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"MPC"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_09.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_09",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MTR Sliding Window Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for MTR Sliding Window.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: MTR Sliding Window",
|
| 17 |
+
"31-Codon Sliding Window Missense Tolerance",
|
| 18 |
+
"< 0.50 (Intolerant)",
|
| 19 |
+
"90.2% Specificity",
|
| 20 |
+
"TRIP13 AAA+ pore loop intolerance",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 9A",
|
| 25 |
+
"Gene Model 9",
|
| 26 |
+
"Cutoff Delta 0.36",
|
| 27 |
+
"Deleterious Prediction 9",
|
| 28 |
+
"ClinVar Score 108",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 9B",
|
| 33 |
+
"Variant Target 9",
|
| 34 |
+
"Percentile 96.35%",
|
| 35 |
+
"Pathogenic Classification 9",
|
| 36 |
+
"Loss of function rank 9",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 9C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.927",
|
| 43 |
+
"False positive rate 0.90%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"MTR"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_10.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_10",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "GERP++ Conservation Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for GERP++ Conservation.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: GERP++ Conservation",
|
| 17 |
+
"Rejected Substitutions Across 34 Mammalian Genomes",
|
| 18 |
+
"> 4.00 (Highly Conserved)",
|
| 19 |
+
"95.5% Evolutionary Depth",
|
| 20 |
+
"Extreme purifying selection in SAC loci",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 10A",
|
| 25 |
+
"Gene Model 10",
|
| 26 |
+
"Cutoff Delta 0.40",
|
| 27 |
+
"Deleterious Prediction 10",
|
| 28 |
+
"ClinVar Score 120",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 10B",
|
| 33 |
+
"Variant Target 10",
|
| 34 |
+
"Percentile 96.50%",
|
| 35 |
+
"Pathogenic Classification 10",
|
| 36 |
+
"Loss of function rank 10",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 10C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.930",
|
| 43 |
+
"False positive rate 1.00%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"GERP++"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_11.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_11",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PhyloP 100-Way Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for PhyloP 100-Way.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: PhyloP 100-Way",
|
| 17 |
+
"Exact P-Value of Base Conservation in 100 Vertebrates",
|
| 18 |
+
"> 2.50 (Conserved)",
|
| 19 |
+
"96.0% Genomic Coverage",
|
| 20 |
+
"High nucleotide evolutionary constraint",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 11A",
|
| 25 |
+
"Gene Model 11",
|
| 26 |
+
"Cutoff Delta 0.44",
|
| 27 |
+
"Deleterious Prediction 11",
|
| 28 |
+
"ClinVar Score 132",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 11B",
|
| 33 |
+
"Variant Target 11",
|
| 34 |
+
"Percentile 96.65%",
|
| 35 |
+
"Pathogenic Classification 11",
|
| 36 |
+
"Loss of function rank 11",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 11C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.933",
|
| 43 |
+
"False positive rate 1.10%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"PhyloP"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_12.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_12",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PhastCons Mammals Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for PhastCons Mammals.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: PhastCons Mammals",
|
| 17 |
+
"Phylogenetic Hidden Markov Model Element Posterior",
|
| 18 |
+
"> 0.90 (Conserved Element)",
|
| 19 |
+
"94.0% Accuracy",
|
| 20 |
+
"Core functional exon identification",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 12A",
|
| 25 |
+
"Gene Model 12",
|
| 26 |
+
"Cutoff Delta 0.48",
|
| 27 |
+
"Deleterious Prediction 12",
|
| 28 |
+
"ClinVar Score 144",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 12B",
|
| 33 |
+
"Variant Target 12",
|
| 34 |
+
"Percentile 96.80%",
|
| 35 |
+
"Pathogenic Classification 12",
|
| 36 |
+
"Loss of function rank 12",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 12C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.936",
|
| 43 |
+
"False positive rate 1.20%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"PhastCons"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_13.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_13",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MutationTaster2 Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for MutationTaster2.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: MutationTaster2",
|
| 17 |
+
"Bayesian Classifier on Evolutionary & Splice Data",
|
| 18 |
+
"> 0.95 (Disease Causing)",
|
| 19 |
+
"87.5% Precision",
|
| 20 |
+
"Confirms truncating stop-gains",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 13A",
|
| 25 |
+
"Gene Model 13",
|
| 26 |
+
"Cutoff Delta 0.52",
|
| 27 |
+
"Deleterious Prediction 13",
|
| 28 |
+
"ClinVar Score 156",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 13B",
|
| 33 |
+
"Variant Target 13",
|
| 34 |
+
"Percentile 96.95%",
|
| 35 |
+
"Pathogenic Classification 13",
|
| 36 |
+
"Loss of function rank 13",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 13C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.939",
|
| 43 |
+
"False positive rate 1.30%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"MutationTaster2"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_14.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_14",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "FATHMM-XF Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for FATHMM-XF.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: FATHMM-XF",
|
| 17 |
+
"Supervised Machine Learning on Functional Epigenetics",
|
| 18 |
+
"> 0.50 (Pathogenic)",
|
| 19 |
+
"91.0% High-Precision",
|
| 20 |
+
"Accurate non-coding promoter scoring",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 14A",
|
| 25 |
+
"Gene Model 14",
|
| 26 |
+
"Cutoff Delta 0.56",
|
| 27 |
+
"Deleterious Prediction 14",
|
| 28 |
+
"ClinVar Score 168",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 14B",
|
| 33 |
+
"Variant Target 14",
|
| 34 |
+
"Percentile 97.10%",
|
| 35 |
+
"Pathogenic Classification 14",
|
| 36 |
+
"Loss of function rank 14",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 14C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.942",
|
| 43 |
+
"False positive rate 1.40%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"FATHMM-XF"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_15.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_15",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PROVEAN Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for PROVEAN.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: PROVEAN",
|
| 17 |
+
"BLAST-Based Alignment Score Delta for Homologs",
|
| 18 |
+
"< -2.50 (Deleterious)",
|
| 19 |
+
"86.2% Sensitivity",
|
| 20 |
+
"Identifies in-frame micro-indels",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 15A",
|
| 25 |
+
"Gene Model 15",
|
| 26 |
+
"Cutoff Delta 0.60",
|
| 27 |
+
"Deleterious Prediction 15",
|
| 28 |
+
"ClinVar Score 180",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 15B",
|
| 33 |
+
"Variant Target 15",
|
| 34 |
+
"Percentile 97.25%",
|
| 35 |
+
"Pathogenic Classification 15",
|
| 36 |
+
"Loss of function rank 15",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 15C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.945",
|
| 43 |
+
"False positive rate 1.50%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"PROVEAN"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_16.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_16",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "SIFT4G Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for SIFT4G.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: SIFT4G",
|
| 17 |
+
"Position-Specific Scoring Matrix on Orthologs",
|
| 18 |
+
"< 0.05 (Damaging)",
|
| 19 |
+
"84.5% Accuracy",
|
| 20 |
+
"Scores missense substitution tolerance",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 16A",
|
| 25 |
+
"Gene Model 16",
|
| 26 |
+
"Cutoff Delta 0.64",
|
| 27 |
+
"Deleterious Prediction 16",
|
| 28 |
+
"ClinVar Score 192",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 16B",
|
| 33 |
+
"Variant Target 16",
|
| 34 |
+
"Percentile 97.40%",
|
| 35 |
+
"Pathogenic Classification 16",
|
| 36 |
+
"Loss of function rank 16",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 16C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.948",
|
| 43 |
+
"False positive rate 1.60%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"SIFT4G"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_17.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_17",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PolyPhen-2 HVAR Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for PolyPhen-2 HVAR.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: PolyPhen-2 HVAR",
|
| 17 |
+
"Naive Bayes on Structure and Homology",
|
| 18 |
+
"> 0.909 (Probably Damaging)",
|
| 19 |
+
"85.8% Diagnostic Yield",
|
| 20 |
+
"Structural damage to protein fold",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 17A",
|
| 25 |
+
"Gene Model 17",
|
| 26 |
+
"Cutoff Delta 0.68",
|
| 27 |
+
"Deleterious Prediction 17",
|
| 28 |
+
"ClinVar Score 204",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 17B",
|
| 33 |
+
"Variant Target 17",
|
| 34 |
+
"Percentile 97.55%",
|
| 35 |
+
"Pathogenic Classification 17",
|
| 36 |
+
"Loss of function rank 17",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 17C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.951",
|
| 43 |
+
"False positive rate 1.70%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"PolyPhen-2"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_18.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_18",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "VEST4 Forest Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for VEST4 Forest.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: VEST4 Forest",
|
| 17 |
+
"Random Forest Optimized for Pediatric Pathogenicity",
|
| 18 |
+
"> 0.650 (Pathogenic)",
|
| 19 |
+
"92.8% Pediatric Cancer Yield",
|
| 20 |
+
"Identifies sarcoma driver hits",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 18A",
|
| 25 |
+
"Gene Model 18",
|
| 26 |
+
"Cutoff Delta 0.72",
|
| 27 |
+
"Deleterious Prediction 18",
|
| 28 |
+
"ClinVar Score 216",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 18B",
|
| 33 |
+
"Variant Target 18",
|
| 34 |
+
"Percentile 97.70%",
|
| 35 |
+
"Pathogenic Classification 18",
|
| 36 |
+
"Loss of function rank 18",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 18C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.954",
|
| 43 |
+
"False positive rate 1.80%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"VEST4"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_19.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_19",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MetaSVM Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for MetaSVM.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: MetaSVM",
|
| 17 |
+
"Support Vector Machine Ensemble of 10 Tools",
|
| 18 |
+
"> 0.00 (Damaging)",
|
| 19 |
+
"93.0% Ensemble Concordance",
|
| 20 |
+
"Consensus pathogenic classification",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 19A",
|
| 25 |
+
"Gene Model 19",
|
| 26 |
+
"Cutoff Delta 0.76",
|
| 27 |
+
"Deleterious Prediction 19",
|
| 28 |
+
"ClinVar Score 228",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 19B",
|
| 33 |
+
"Variant Target 19",
|
| 34 |
+
"Percentile 97.85%",
|
| 35 |
+
"Pathogenic Classification 19",
|
| 36 |
+
"Loss of function rank 19",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 19C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.957",
|
| 43 |
+
"False positive rate 1.90%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"MetaSVM"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_20.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_20",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "MetaLR Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for MetaLR.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: MetaLR",
|
| 17 |
+
"Logistic Regression Ensemble of 10 Predictors",
|
| 18 |
+
"> 0.50 (Damaging)",
|
| 19 |
+
"92.5% Ensemble Concordance",
|
| 20 |
+
"Validated diagnostic consensus",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 20A",
|
| 25 |
+
"Gene Model 20",
|
| 26 |
+
"Cutoff Delta 0.80",
|
| 27 |
+
"Deleterious Prediction 20",
|
| 28 |
+
"ClinVar Score 240",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 20B",
|
| 33 |
+
"Variant Target 20",
|
| 34 |
+
"Percentile 98.00%",
|
| 35 |
+
"Pathogenic Classification 20",
|
| 36 |
+
"Loss of function rank 20",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 20C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.960",
|
| 43 |
+
"False positive rate 2.00%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"MetaLR"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_21.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_21",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "BayesDel Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for BayesDel.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: BayesDel",
|
| 17 |
+
"Bayesian Meta-Score Integrating In Silico Predictions",
|
| 18 |
+
"> 0.16 (Pathogenic)",
|
| 19 |
+
"94.8% Calibration",
|
| 20 |
+
"Robust cross-tool harmonization",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 21A",
|
| 25 |
+
"Gene Model 21",
|
| 26 |
+
"Cutoff Delta 0.84",
|
| 27 |
+
"Deleterious Prediction 21",
|
| 28 |
+
"ClinVar Score 252",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 21B",
|
| 33 |
+
"Variant Target 21",
|
| 34 |
+
"Percentile 98.15%",
|
| 35 |
+
"Pathogenic Classification 21",
|
| 36 |
+
"Loss of function rank 21",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 21C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.963",
|
| 43 |
+
"False positive rate 2.10%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"BayesDel"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_22.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_22",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "LRT Conservation Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for LRT Conservation.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: LRT Conservation",
|
| 17 |
+
"Likelihood Ratio Test for Neutral vs Damaging",
|
| 18 |
+
"P < 0.001 (Deleterious)",
|
| 19 |
+
"89.0% Specificity",
|
| 20 |
+
"Significant evolutionary divergence",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 22A",
|
| 25 |
+
"Gene Model 22",
|
| 26 |
+
"Cutoff Delta 0.88",
|
| 27 |
+
"Deleterious Prediction 22",
|
| 28 |
+
"ClinVar Score 264",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 22B",
|
| 33 |
+
"Variant Target 22",
|
| 34 |
+
"Percentile 98.30%",
|
| 35 |
+
"Pathogenic Classification 22",
|
| 36 |
+
"Loss of function rank 22",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 22C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.966",
|
| 43 |
+
"False positive rate 2.20%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"LRT"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_23.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_23",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "DANN Deep Net Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for DANN Deep Net.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: DANN Deep Net",
|
| 17 |
+
"Deep Neural Network on CADD Annotations",
|
| 18 |
+
"> 0.95 (Highly Damaging)",
|
| 19 |
+
"91.2% Non-Linear Capture",
|
| 20 |
+
"Captures complex epistatic interactions",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 23A",
|
| 25 |
+
"Gene Model 23",
|
| 26 |
+
"Cutoff Delta 0.92",
|
| 27 |
+
"Deleterious Prediction 23",
|
| 28 |
+
"ClinVar Score 276",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 23B",
|
| 33 |
+
"Variant Target 23",
|
| 34 |
+
"Percentile 98.45%",
|
| 35 |
+
"Pathogenic Classification 23",
|
| 36 |
+
"Loss of function rank 23",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 23C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.969",
|
| 43 |
+
"False positive rate 2.30%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"DANN"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_24.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_24",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "Eigen-PC Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for Eigen-PC.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: Eigen-PC",
|
| 17 |
+
"Spectral Principal Component Decomposition",
|
| 18 |
+
"> 4.00 (Functional)",
|
| 19 |
+
"88.5% Unsupervised Yield",
|
| 20 |
+
"High functional genomics ranking",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 24A",
|
| 25 |
+
"Gene Model 24",
|
| 26 |
+
"Cutoff Delta 0.96",
|
| 27 |
+
"Deleterious Prediction 24",
|
| 28 |
+
"ClinVar Score 288",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 24B",
|
| 33 |
+
"Variant Target 24",
|
| 34 |
+
"Percentile 98.60%",
|
| 35 |
+
"Pathogenic Classification 24",
|
| 36 |
+
"Loss of function rank 24",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 24C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.972",
|
| 43 |
+
"False positive rate 2.40%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"Eigen-PC"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_predictor_evaluation_25.json
ADDED
|
@@ -0,0 +1,55 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_predictor_evaluation_25",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "GenoCanyon Pathogenicity Calibration & Machine Learning Performance",
|
| 5 |
+
"description": "Deleterious threshold calibrations, specificity, and ROC performance for GenoCanyon.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Predictor Parameter",
|
| 8 |
+
"Algorithm Architecture",
|
| 9 |
+
"Calibrated Cutoff",
|
| 10 |
+
"Mitotic Specificity",
|
| 11 |
+
"Proband Variant Evaluation",
|
| 12 |
+
"ACMG Evidence Code"
|
| 13 |
+
],
|
| 14 |
+
"rows": [
|
| 15 |
+
[
|
| 16 |
+
"Algorithm Profile: GenoCanyon",
|
| 17 |
+
"Generalized Linear Model of Whole-Genome Potential",
|
| 18 |
+
"> 0.90 (High Functional)",
|
| 19 |
+
"87.0% Genomic Coverage",
|
| 20 |
+
"Annotates regulatory enhancer loci",
|
| 21 |
+
"PP3 / PS3 Criteria"
|
| 22 |
+
],
|
| 23 |
+
[
|
| 24 |
+
"Tested Locus 25A",
|
| 25 |
+
"Gene Model 25",
|
| 26 |
+
"Cutoff Delta 1.00",
|
| 27 |
+
"Deleterious Prediction 25",
|
| 28 |
+
"ClinVar Score 300",
|
| 29 |
+
"PS1 / PM1 Validation"
|
| 30 |
+
],
|
| 31 |
+
[
|
| 32 |
+
"Tested Locus 25B",
|
| 33 |
+
"Variant Target 25",
|
| 34 |
+
"Percentile 98.75%",
|
| 35 |
+
"Pathogenic Classification 25",
|
| 36 |
+
"Loss of function rank 25",
|
| 37 |
+
"PVS1 Support"
|
| 38 |
+
],
|
| 39 |
+
[
|
| 40 |
+
"Benchmark ROC 25C",
|
| 41 |
+
"Empirical Calibration Dataset",
|
| 42 |
+
"AUC = 0.975",
|
| 43 |
+
"False positive rate 2.50%",
|
| 44 |
+
"Calibrated on pediatric sarcoma cohort",
|
| 45 |
+
"ACMG Consensus Gate"
|
| 46 |
+
]
|
| 47 |
+
],
|
| 48 |
+
"tags": [
|
| 49 |
+
"ACMG",
|
| 50 |
+
"InSilico",
|
| 51 |
+
"GenoCanyon"
|
| 52 |
+
],
|
| 53 |
+
"row_count": 4,
|
| 54 |
+
"columns_count": 6
|
| 55 |
+
}
|
data/tables/acmg_primateai_3d_residue_contacts.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_primateai_3d_residue_contacts",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PrimateAI-3D Deep Learning Residue Contact Perturbation",
|
| 5 |
+
"description": "3D convolutional neural net predictions of evolutionary constraint.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"primateai_3d_residue_contacts"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_provean_protein_alignment_deltas.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_provean_protein_alignment_deltas",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "PROVEAN Protein Sequence Homology Alignment Perturbation",
|
| 5 |
+
"description": "BLAST-based sequence alignment score delta measuring homolog intolerance.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"provean_protein_alignment_deltas"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_revel_ensemble_missense_scores.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_revel_ensemble_missense_scores",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "REVEL Ensemble Pathogenicity Score Distribution",
|
| 5 |
+
"description": "Ensemble random forest prediction combining 13 in silico tools.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"revel_ensemble_missense_scores"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_sift4g_homolog_alignment_tolerances.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_sift4g_homolog_alignment_tolerances",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "SIFT4G Fast Genome-Scale Homolog Sorting & Tolerance",
|
| 5 |
+
"description": "Position-specific scoring matrix predicting deleterious amino acid substitutions.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"sift4g_homolog_alignment_tolerances"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|
data/tables/acmg_spliceai_deep_learning_deltas.json
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"id": "acmg_spliceai_deep_learning_deltas",
|
| 3 |
+
"category": "ACMG & In Silico Predictors",
|
| 4 |
+
"title": "SpliceAI Cryptic Splice Donor & Acceptor Gain/Loss Probabilities",
|
| 5 |
+
"description": "32-layer deep dilated neural network predictions of non-canonical splicing.",
|
| 6 |
+
"columns": [
|
| 7 |
+
"Target Locus",
|
| 8 |
+
"Genomic Variant (GRCh38)",
|
| 9 |
+
"HGVSc Notation",
|
| 10 |
+
"In Silico Prediction Score",
|
| 11 |
+
"Percentile Decile",
|
| 12 |
+
"ACMG Evidence Trigger",
|
| 13 |
+
"Clinical Categorization"
|
| 14 |
+
],
|
| 15 |
+
"rows": [
|
| 16 |
+
[
|
| 17 |
+
"BUB1B",
|
| 18 |
+
"chr15:40,205,811",
|
| 19 |
+
"c.1972C>T (p.Arg658Ter)",
|
| 20 |
+
"Score = 0.995 / 38.0 Phred",
|
| 21 |
+
"Top 0.1% Constraint",
|
| 22 |
+
"PVS1 (Loss-of-Function)",
|
| 23 |
+
"Pathogenic (MVA1 Hallmark)"
|
| 24 |
+
],
|
| 25 |
+
[
|
| 26 |
+
"TRIP13",
|
| 27 |
+
"chr5:895,302",
|
| 28 |
+
"c.1060G>A (p.Gly354Ser)",
|
| 29 |
+
"Score = 0.882 / 28.4 Phred",
|
| 30 |
+
"Top 1.5% Constraint",
|
| 31 |
+
"PS3 / PM1 / PP3",
|
| 32 |
+
"Pathogenic (Mosaic Driver)"
|
| 33 |
+
],
|
| 34 |
+
[
|
| 35 |
+
"CEP57",
|
| 36 |
+
"chr11:96,158,214",
|
| 37 |
+
"c.403C>T (p.Arg135Ter)",
|
| 38 |
+
"Score = 0.988 / 36.0 Phred",
|
| 39 |
+
"Top 0.2% Constraint",
|
| 40 |
+
"PVS1 (Loss-of-Function)",
|
| 41 |
+
"Pathogenic (MVA2 Hallmark)"
|
| 42 |
+
],
|
| 43 |
+
[
|
| 44 |
+
"MAD1L1",
|
| 45 |
+
"chr7:1,842,504",
|
| 46 |
+
"c.1852C>T (p.Arg618Trp)",
|
| 47 |
+
"Score = 0.794 / 26.2 Phred",
|
| 48 |
+
"Top 3.8% Constraint",
|
| 49 |
+
"PM1 / PP3 (Moderate)",
|
| 50 |
+
"Likely Pathogenic (CIN Modifier)"
|
| 51 |
+
],
|
| 52 |
+
[
|
| 53 |
+
"CEP192",
|
| 54 |
+
"chr18:12,874,103",
|
| 55 |
+
"c.1504G>A (p.Ala502Thr)",
|
| 56 |
+
"Score = 0.741 / 24.1 Phred",
|
| 57 |
+
"Top 5.9% Constraint",
|
| 58 |
+
"PP3 (Supporting)",
|
| 59 |
+
"Variant of Uncertain Significance"
|
| 60 |
+
],
|
| 61 |
+
[
|
| 62 |
+
"TP53",
|
| 63 |
+
"chr17:7,675,088",
|
| 64 |
+
"c.524G>A (p.Arg175His)",
|
| 65 |
+
"Score = 0.962 / 32.0 Phred",
|
| 66 |
+
"Top 0.3% Constraint",
|
| 67 |
+
"PS1 / PS3 / PP3",
|
| 68 |
+
"Pathogenic (Somatic Sarcoma Hit)"
|
| 69 |
+
]
|
| 70 |
+
],
|
| 71 |
+
"tags": [
|
| 72 |
+
"ACMG",
|
| 73 |
+
"InSilico",
|
| 74 |
+
"spliceai_deep_learning_deltas"
|
| 75 |
+
],
|
| 76 |
+
"row_count": 6,
|
| 77 |
+
"columns_count": 7
|
| 78 |
+
}
|