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cgpu/sample.json

Created July 5, 2021 12:09
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sample.json
[
{
"acmg_annotation.classifications.user_explain": [
"Null variant (frame-shift), in gene FOXO6, for which loss-of-function is a known mechanism of disease (gnomAD Loss-of-Function Observed/Expected = 0.213 is less than 0.763).",
"Variant not found in gnomAD exomes (unable to check gnomAD exomes coverage).",
"Pathogenic computational verdict based on 1 pathogenic prediction from phyloP vs no benign predictions."
],
"acmg_annotation.coding_impact": "frameshift",
"acmg_annotation.gene_id": 8339,
"acmg_annotation.gene_symbol": "FOXO6",
"acmg_annotation.verdict.ACMG_rules.approx_score": 80,
"acmg_annotation.verdict.ACMG_rules.benign_subscore": "Uncertain Significance",
"acmg_annotation.verdict.ACMG_rules.pathogenic_subscore": "Pathogenic",
"acmg_annotation.verdict.ACMG_rules.verdict": "Pathogenic",
"acmg_annotation.version_name": "9.4.6",
"Allelic balance": 0.918918918918919,
"all1": "GGCCCGCGCCGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCC",
"all2": "CTT",
"alt": "C",
"amp_annotation.classifications": {},
"amp_annotation.classifications.name": {},
"amp_annotation.classifications.tier": {},
"amp_annotation.classifications.user_explain.Tier I": {},
"amp_annotation.classifications.user_explain.Tier II": {},
"amp_annotation.classifications.user_explain.Tier III": {},
"amp_annotation.classifications.user_explain.Tier IV": {},
"amp_annotation.verdict": {},
"amp_annotation.verdict.approx_score": {},
"amp_annotation.verdict.tier": {},
"amp_annotation.version_name": {},
"cadd.cadd_score": {},
"cancer_hotspots.biotype": {},
"cancer_hotspots.cancer_name.key": {},
"cancer_hotspots.canonical": {},
"cancer_hotspots.total_samples": {},
"cbio": {},
"cbio_portal.ajcc_pathologic_tumor_stage.key": {},
"cbio_portal.cancer_name.key": {},
"cbio_portal.canonical": {},
"cbio_portal.grade": {},
"cbio_portal.hotspot": {},
"chromosome": "chr5",
"Coverage": 37,
"cytobands": "1p34.2",
"dbnsfp_dbscsnv": {},
"dbnsfp.aloft_confidence": {},
"dbnsfp.aloft_pred": {},
"dbnsfp.aloft_prob_dominant": {},
"dbnsfp.aloft_prob_recessive": {},
"dbnsfp.aloft_prob_tolerant": {},
"dbnsfp.cadd_phred": {},
"dbnsfp.cadd_raw": {},
"dbnsfp.cadd_raw_rankscore": {},
"dbnsfp.deogen2_pred": {},
"dbnsfp.ensembl_proteinid": {},
"dbnsfp.ensembl_transcriptid": {},
"dbnsfp.fathmm_mkl_coding_pred": {},
"dbnsfp.fathmm_pred": {},
"dbnsfp.lrt_pred": {},
"dbnsfp.metalr_pred": {},
"dbnsfp.metasvm_pred": {},
"dbnsfp.mutationassessor_pred": {},
"dbnsfp.mutationtaster_pred": {},
"dbnsfp.mutpred_score": {},
"dbnsfp.phastcons100way_vertebrate": {},
"dbnsfp.phastcons100way_vertebrate_rankscore": {},
"dbnsfp.phylop100way_vertebrate": {},
"dbnsfp.phylop100way_vertebrate_rankscore": {},
"dbnsfp.polyphen2_hdiv_pred": {},
"dbnsfp.polyphen2_hvar_pred": {},
"dbnsfp.primateai_pred": {},
"dbnsfp.provean_pred": {},
"dbnsfp.revel_score": {},
"dbnsfp.sift_pred": {},
"dbnsfp.sift4g_pred": {},
"ensembl_transcripts": {
"items": [
{
"canonical": true,
"coding_impact": "frameshift",
"coding_location": "336 of 492",
"ensembl_support_level": null,
"function": [
"coding",
"splicing"
],
"gene_symbol": "FOXO6",
"hgvs": "c.1007_1008insGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCCGCCCGCGCC",
"hgvs_p1": "R337Gfs*106",
"hgvs_p3": "p.Arg337GlyfsTer106",
"location": "exon 3 of 3 before position 9 of 477",
"name": "ENST00000641094.1",
"splice_distance": "9",
"strand": "+"
},
{
"canonical": false,
"coding_impact": null,
"coding_location": null,
"ensembl_support_level": "5",
"function": [
"non-coding exon"
],
"gene_symbol": "FOXO6",
"hgvs": null,
"hgvs_p1": null,
"hgvs_p3": null,
"location": "exon 2 of 2 before position 595 of 1975",
"name": "ENST00000372591.1",
"splice_distance": "595",
"strand": "+"
}
],
"version": "103"
},
"genotype": "1/1",
"gnomad_exomes.ac": {},
"gnomad_exomes.ac_afr": {},
"gnomad_exomes.ac_afr_female": {},
"gnomad_exomes.ac_afr_male": {},
"gnomad_exomes.ac_amr": {},
"gnomad_exomes.ac_amr_female": {},
"gnomad_exomes.ac_amr_male": {},
"gnomad_exomes.ac_asj": {},
"gnomad_exomes.ac_asj_female": {},
"gnomad_exomes.ac_asj_male": {},
"gnomad_exomes.ac_eas": {},
"gnomad_exomes.ac_eas_female": {},
"gnomad_exomes.ac_eas_jpn": {},
"gnomad_exomes.ac_eas_kor": {},
"gnomad_exomes.ac_eas_male": {},
"gnomad_exomes.ac_eas_oea": {},
"gnomad_exomes.ac_female": {},
"gnomad_exomes.ac_fin": {},
"gnomad_exomes.ac_fin_female": {},
"gnomad_exomes.ac_fin_male": {},
"gnomad_exomes.ac_male": {},
"gnomad_exomes.ac_nfe": {},
"gnomad_exomes.ac_nfe_bgr": {},
"gnomad_exomes.ac_nfe_est": {},
"gnomad_exomes.ac_nfe_female": {},
"gnomad_exomes.ac_nfe_male": {},
"gnomad_exomes.ac_nfe_nwe": {},
"gnomad_exomes.ac_nfe_onf": {},
"gnomad_exomes.ac_nfe_seu": {},
"gnomad_exomes.ac_nfe_swe": {},
"gnomad_exomes.ac_oth": {},
"gnomad_exomes.ac_oth_female": {},
"gnomad_exomes.ac_oth_male": {},
"gnomad_exomes.ac_sas": {},
"gnomad_exomes.ac_sas_female": {},
"gnomad_exomes.ac_sas_male": {},
"gnomad_exomes.af": {},
"gnomad_genomes.ac": 132281,
"gnomad_genomes.ac_afr": 39538,
"gnomad_genomes.ac_afr_female": 21339,
"gnomad_genomes.ac_afr_male": 18199,
"gnomad_genomes.ac_ami": 862,
"gnomad_genomes.ac_ami_female": 446,
"gnomad_genomes.ac_ami_male": 416,
"gnomad_genomes.ac_amr": 12763,
"gnomad_genomes.ac_amr_female": 5506,
"gnomad_genomes.ac_amr_male": 7257,
"gnomad_genomes.ac_asj": 3128,
"gnomad_genomes.ac_asj_female": 1646,
"gnomad_genomes.ac_asj_male": 1482,
"gnomad_genomes.ac_eas": 2935,
"gnomad_genomes.ac_eas_female": 1373,
"gnomad_genomes.ac_eas_male": 1562,
"gnomad_genomes.ac_female": 68535,
"gnomad_genomes.ac_fin": 7682,
"gnomad_genomes.ac_fin_female": 1094,
"gnomad_genomes.ac_fin_male": 6588,
"gnomad_genomes.ac_male": 63746,
"gnomad_genomes.ac_nfe": 60498,
"gnomad_genomes.ac_nfe_female": 35568,
"gnomad_genomes.ac_nfe_male": 24930,
"gnomad_genomes.ac_oth": 1997,
"gnomad_genomes.ac_oth_female": 1027,
"gnomad_genomes.ac_oth_male": 970,
"gnomad_genomes.ac_sas": 2878,
"gnomad_genomes.ac_sas_female": 536,
"gnomad_genomes.ac_sas_male": 2342,
"gnomad_genomes.af": 0.9972182434979269,
"gwas.items.disease_or_trait": {},
"gwas.items.initial_sample_size": {},
"gwas.items.odds_ratio": {},
"gwas.items.p_value": {},
"gwas.items.pub_med_references": {},
"ncbi_clinvar2.accessions.clinical_significance": {},
"ncbi_clinvar2.accessions.date_created": {},
"ncbi_clinvar2.accessions.diseases": {},
"ncbi_clinvar2.accessions.drug_response": {},
"ncbi_clinvar2.accessions.drug_response.names": {},
"ncbi_clinvar2.accessions.drug_response.pub_med_references": {},
"ncbi_clinvar2.accessions.review_date": {},
"pos": "54645453",
"ref": "G",
"refseq_transcripts.items.gene_symbol": "FOXO6",
"refseq_transcripts.items.hgvs": "c.1008_1008+1insGGGACGCCCGCCTACTTCGGCGGCTGCAAGGGCGGCGCCTACGGCGGGGGCGGGGGCTTCGGGCCGCCGGCGATGGGCGCTCTGCGCCGTCTGCCCATGCAGACCATCCAGGAGAACAAGCAGGCCAGCTTCGTGCCGGCCGCGGCGCCCTTCCGCCCTGGGGCGCTGCCCGCGCTGCTGCCGCCGCCGCCGCCCGCGCC",
"regions.NCBI ClinVar CNVs": {
"11-May-2021": [
{
"ClinVarRegionJson": {
"accessions": [
{
"accession_id": "RCV000138891",
"allele_id": 159714,
"clinical_significance": [
"Pathogenic"
],
"date_created": 20140830,
"review_date": 20120601,
"review_description": "Pathogenic",
"review_stars": 0,
"review_status": "no assertion criteria provided",
"submission_description": [
""
],
"submissions": [
{
"accession_id": "SCV000179329",
"clinical_significance": [
"Pathogenic"
],
"date_updated": 20200326,
"finding": [
{
"names": [
"Intellectual Disability"
],
"symbols": {
"HP": "HP:0001249"
}
}
],
"origin": "not provided",
"review_date": 20120601,
"review_description": "Pathogenic",
"review_status": "no assertion criteria provided",
"submission_description": [
""
],
"submitter_date": 20170926,
"submitter_name": "ISCA site 1"
}
],
"title": "GRCh38/hg38 1p36.11-34.2(chr1:24381206-41401517)x3 AND See cases",
"variation_id": 149963
}
],
"acmg_class": "Pathogenic",
"allele_id": 159714,
"clinical_significance": [
"Pathogenic"
],
"date_created": 20210428,
"identifiers": {
"dbVar": "nsv916207"
},
"last_evaluation": 20210428,
"names": [
"GRCh38/hg38 1p36.11-34.2(chr1:24381206-41401517)x3"
],
"num_submissions": 1,
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"review_status": "no assertion criteria provided",
"type": "copy number gain",
"variation_id": 149963
},
"chromo": "chr1",
"length": 17020311,
"position": 24381206
},
{
"ClinVarRegionJson": {
"accessions": [
{
"accession_id": "RCV000053805",
"allele_id": 74529,
"clinical_significance": [
"Pathogenic"
],
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"review_date": 20110812,
"review_description": "Pathogenic",
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"review_status": "criteria provided, single submitter",
"submission_description": [
""
],
"submissions": [
{
"accession_id": "SCV000081168",
"clinical_significance": [
"Pathogenic"
],
"date_updated": 20200801,
"finding": [
{
"names": [
"Global Developmental Delay"
],
"symbols": {
"HP": "HP:0001263"
}
}
],
"method": "clinical testing",
"origin": "not provided",
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"review_description": "Pathogenic",
"review_status": "criteria provided, single submitter",
"submission_description": [
""
],
"submitter_date": 20140621,
"submitter_name": "ISCA site 4"
}
],
"title": "GRCh38/hg38 1p34.3-34.2(chr1:38108665-42327551)x1 AND See cases",
"variation_id": 59934
}
],
"acmg_class": "Pathogenic",
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"date_created": 20201126,
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"names": [
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"type": "copy number loss",
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{
"ClinVarRegionJson": {
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{
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""
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]
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{
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""
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""
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{
"ClinVarRegionJson": {
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{
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""
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{
"accession_id": "SCV000183564",
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"finding": [
{
"names": [
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],
"symbols": {
"HP": "HP:0000717"
}
},
{
"names": [
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"HP": "HP:0000750"
}
},
{
"names": [
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},
{
"names": [
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"HP": "HP:0001250"
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},
{
"names": [
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"HP": "HP:0001257"
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},
{
"names": [
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"HP": "HP:0001263"
}
},
{
"names": [
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"HP": "HP:0001371"
}
},
{
"names": [
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"HP": "HP:0002194"
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}
],
"origin": "not provided",
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"submission_description": [
""
],
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}
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"title": "GRCh38/hg38 1p34.2(chr1:40834404-43123071)x1 AND See cases",
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}
],
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"type": "copy number loss",
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},
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}
]
},
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"regions.NIH GTEx.v8.GTExJsonData.expressions.Adipose - Visceral (Omentum)": 0.037281800000000004,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Adrenal Gland": 0.03302460000000001,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Artery - Aorta": 0.12018000000000001,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Artery - Coronary": 0.06506330000000002,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Artery - Tibial": 0.09259160000000004,
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"regions.NIH GTEx.v8.GTExJsonData.expressions.Brain - Anterior cingulate cortex (BA24)": 0.11726200000000003,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Brain - Caudate (basal ganglia)": 0.15838100000000002,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Brain - Cerebellar Hemisphere": 0.024616900000000004,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Brain - Cerebellum": 0.027108600000000007,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Brain - Cortex": 0.07941370000000002,
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"regions.NIH GTEx.v8.GTExJsonData.expressions.Pituitary": 0.006151140000000002,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Prostate": 0.008787350000000003,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Skin - Not Sun Exposed (Suprapubic)": 0.0032220300000000007,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Skin - Sun Exposed (Lower leg)": 0.0029291200000000003,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Small Intestine - Terminal Ileum": 0.16157500000000002,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Spleen": 0.8664280000000001,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Stomach": 0.005272410000000001,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Testis": 0.00117165,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Thyroid": 0.003514940000000001,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Uterus": 0.0023432900000000005,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Vagina": 0.004100760000000001,
"regions.NIH GTEx.v8.GTExJsonData.expressions.Whole Blood": 0.11879500000000004,
"variant_type": "SNV",
"vcf_barcode": "sample",
"zygosity": "Heterozygous"
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{
"acmg_annotation.classifications.user_explain": [
"Null variant (intronic within ±2 of splice site), in gene TPP1, for which loss-of-function is a known mechanism of disease (gnomAD Loss-of-Function Observed/Expected = 0.508 is less than 0.763), associated with Ceroid lipofuscinosis, neuronal, 2 and Spinocerebellar ataxia, autosomal recessive 7.",
[
"GnomAD exomes homozygous allele count = 0 is less than 3 for recessive gene TPP1 (unable to check gnomAD exomes coverage).",
"Variant not found in gnomAD genomes (good gnomAD genomes coverage = 31.0)."
],
[
"ClinVar classifies this variant as Pathogenic, rated 2 stars, multiple submissions with no conflicts.",
"Using strength Moderate because of the evidence presented by ClinVar."
],
"Pathogenic computational verdict based on 7 pathogenic predictions from BayesDel_addAF, CADD, DANN, EIGEN, FATHMM-MKL, MutationTaster and scSNV-Splicing vs no benign predictions."
],
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"acmg_annotation.gene_symbol": "TPP1",
"acmg_annotation.verdict.ACMG_rules.approx_score": 100,
"acmg_annotation.verdict.ACMG_rules.benign_subscore": "Uncertain Significance",
"acmg_annotation.verdict.ACMG_rules.pathogenic_subscore": "Pathogenic",
"acmg_annotation.verdict.ACMG_rules.verdict": "Pathogenic",
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"all1": "C",
"all2": "T",
"alt": "GGGTTGGAGAGAGGATGCCTTTGGCA",
"amp_annotation.classifications": {},
"amp_annotation.classifications.name": {},
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"amp_annotation.classifications.user_explain.Tier I": {},
"amp_annotation.classifications.user_explain.Tier II": {},
"amp_annotation.classifications.user_explain.Tier III": {},
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"value": 2
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"chromosome": "chr2",
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{
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}
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