Variant Annotation
Available parameters and response documentation is available here
GET /lookup/chr17:7578443:A:T?add-AMP-annotation=1
{ "chromosome": "chr17", "alt": "T", "ref": "A", "pos": 7578443, "variant_id": "10190170075784430004", "regions": { "uniprot_regions": { "version": "03-Jun-2024", "items": [ { "absolute_positon": 1076661175, "amino_acid": "M1-L25,L25-L32,S33-T125,Y126-G187,G187-E224,V225-S261,S261-A307,A307-Q331,I332-S367,S367-D393", "chromo": "chr17", "colour": "255,0,0", "description": null, "length": 9166, "position": 7571731, "protein": "P53_HUMAN", "type": "homo_sapiens proteome sequences", "pub_med_references": null }, { "absolute_positon": 1076661183, "amino_acid": "M1-L25,L25-L32,S33-T125,Y126-G187,G187-E224,V225-S261,S261-A307,A307-Q331,I332-S367,S367-D393", "chromo": "chr17", "colour": "255,0,0", "description": null, "length": 19007, "position": 7571739, "protein": "P53_HUMAN", "type": "homo_sapiens proteome sequences", "pub_med_references": null }, { "absolute_positon": 1076661183, "amino_acid": "M1-L25,L25-L32,S33-T125,Y126-G187,G187-E224,V225-S261,S261-A307,A307-Q331,I332-S367,S367-D393", "chromo": "chr17", "colour": "255,0,0", "description": null, "length": 19067, "position": 7571739, "protein": "P53_HUMAN", "type": "homo_sapiens proteome sequences", "pub_med_references": null }, { "absolute_positon": 1076661183, "amino_acid": "M1-L25,L25-L32,S33-T125,Y126-G187,G187-E224,V225-S261,S261-A307,A307-Q331,I332-S367,S367-D393", "chromo": "chr17", "colour": "255,0,0", "description": null, "length": 19070, "position": 7571739, "protein": "P53_HUMAN", "type": "homo_sapiens proteome sequences", "pub_med_references": null }, { "absolute_positon": 1076662443, "amino_acid": "Q100-K370", "chromo": "chr17", "colour": "255,102,0", "description": "Interaction with HIPK1", "length": 6391, "position": 7572999, "protein": "P53_HUMAN", "type": "region of interest", "pub_med_references": null }, { "absolute_positon": 1076666330, "amino_acid": "M1-K320", "chromo": "chr17", "colour": "255,102,0", "description": "Interaction with CCAR2", "length": 3027, "position": 7576886, "protein": "P53_HUMAN", "type": "region of interest", "pub_med_references": null }, { "absolute_positon": 1076666482, "amino_acid": "Q100-P300", "chromo": "chr17", "colour": "255,102,0", "description": "Required for interaction with ZNF385A", "length": 2352, "position": 7577038, "protein": "P53_HUMAN", "type": "region of interest", "pub_med_references": null }, { "absolute_positon": 1076666506, "amino_acid": "S116-K292", "chromo": "chr17", "colour": "255,102,0", "description": "Interaction with AXIN1", "length": 2280, "position": 7577062, "protein": "P53_HUMAN", "type": "region of interest", "pub_med_references": null }, { "absolute_positon": 1076666506, "amino_acid": "T102-K292", "chromo": "chr17", "colour": "0,153,51", "description": "DNA-binding region_102-292", "length": 2322, "position": 7577062, "protein": "P53_HUMAN", "type": "DNA-binding domain", "pub_med_references": null }, { "absolute_positon": 1076667017, "amino_acid": "F113-Y236", "chromo": "chr17", "colour": "255,102,0", "description": "Required for interaction with FBXO42", "length": 1778, "position": 7577573, "protein": "P53_HUMAN", "type": "region of interest", "pub_med_references": null } ] }, "nih_gtex": { "version": "v8", "items": [ { "GTExJsonData": { "exon_id": "ENSG00000141510.16_4", "exon_number": "4", "expressions": { "adipose_subcutaneous": 0.37680500000000006, "adipose_visceral_omentum": 0.299737, "adrenal_gland": 0.257683, "artery_aorta": 0.256266, "artery_coronary": 0.275421, "artery_tibial": 0.31053800000000004, "bladder": 0.3452680000000001, "brain_amygdala": 0.0660878, "brain_anterior_cingulate_cortex_ba24": 0.06177650000000001, "brain_caudate_basal_ganglia": 0.08440740000000001, "brain_cerebellar_hemisphere": 0.027807600000000005, "brain_cerebellum": 0.032491900000000004, "brain_cortex": 0.08043920000000002, "brain_frontal_cortex_ba9": 0.05436210000000002, "brain_hippocampus": 0.048782700000000005, "brain_hypothalamus": 0.05058780000000001, "brain_nucleus_accumbens_basal_ganglia": 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0.10851500000000001, "prostate": 0.23776700000000003, "skin_not_sun_exposed_suprapubic": 0.52463, "skin_sun_exposed_lower_leg": 0.560359, "small_intestine_terminal_ileum": 0.3126860000000001, "spleen": 0.33345300000000005, "stomach": 0.21154100000000003, "testis": 0.19945700000000005, "thyroid": 0.24206300000000003, "uterus": 0.38565200000000005, "vagina": 0.34444700000000006, "whole_blood": 0.14136500000000002 }, "gencode_id": "ENSG00000141510", "gene": "TP53", "gene_model_positions": { "chromosome": "chr17", "end": 7580752, "start": 7565097, "strand": "-" }, "gene_positions": { "chromosome": "chr17", "end": 7590868, "start": 7565097, "strand": "-" } }, "absolute_positon": 1076667816, "chromo": "chr17", "length": 440, "position": 7578372 } ] } }, "variant_type": "SNV", "cytobands": "17p13.1", "refseq_transcripts": [ { "items": [ { "name": "NM_000546.6", "strand": "-", "coding_impact": "missense", "function": [ "coding" ], "hgvs": "c.487T>A", "hgvs_p1": "Y163N", "hgvs_p3": 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null, "uniprot_id": null }, { "name": "NM_001126116.2", "strand": "-", "coding_impact": "missense", "function": [ "coding" ], "hgvs": "c.91T>A", "hgvs_p1": "Y31N", "hgvs_p3": "p.(Tyr31Asn)", "location": "exon 1 of 8 position 120 of 192", "coding_location": "31 of 210", "canonical": false, "gene_symbol": "TP53", "splice_distance": "-73", "ensembl_support_level": null, "ensembl_appris": null, "mane_select": null, "mane_plus": null, "uniprot_id": null }, { "name": "NM_001126117.2", "strand": "-", "coding_impact": "missense", "function": [ "coding" ], "hgvs": "c.91T>A", "hgvs_p1": "Y31N", "hgvs_p3": "p.(Tyr31Asn)", "location": "exon 1 of 8 position 120 of 192", "coding_location": "31 of 215", "canonical": false, "gene_symbol": "TP53", "splice_distance": "-73", "ensembl_support_level": null, "ensembl_appris": null, "mane_select": null, "mane_plus": null, "uniprot_id": null }, { "name": "NM_001126118.2", "strand": "-", "coding_impact": "missense", "function": [ "coding" ], "hgvs": 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26389258, 26324357 ], "names": [ "Li-Fraumeni Syndrome" ] } ], "review_date": 20240214, "review_description": "Likely pathogenic", "title": "NM_000546.6(TP53):c.487T>A (p.Tyr163Asn) AND Li-Fraumeni syndrome 1", "review_status": "criteria provided, single submitter", "submission_description": [], "submissions": [ { "submitter_name": "Myriad Genetics, Inc.", "submission_description": [ "This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 10229196, 29979965]. This variant is expected to disrupt protein structure [Myriad internal data]." ], "review_status": "criteria provided, single submitter", "submitter_date": 20240422, "review_description": "Likely pathogenic", "method": "clinical testing", "review_date": 20240214, "origin": "unknown", "diseases": [ { "symbols": { "omim": "151623" } } ], "date_updated": 20240501, "clinical_significance": [ "Likely pathogenic" ], "accession_id": "SCV004932800" } ], "variant_id": 10190170075784430004 }, { "variation_id": 376679, "accession_id": "RCV002338982", "clinical_significance": [ "Likely pathogenic" ], "allele_id": 363558, "date_created": 20221129, "review_stars": 1, "diseases": [ { "normalized_disease": [ "Hereditary Neoplastic Syndrome" ], "normalized_cancer": [ "Tumor predisposition", "Cancer predisposition", "Hereditary Cancer Syndrome" ], "symbols": { "medgen": "C0027672", "mesh": "D009386", "mondo": "MONDO:0015356" }, "pub_med": [ 25394175 ], "names": [ "Hereditary Cancer-Predisposing Syndrome", "Hereditary Neoplastic Syndrome", "Tumor Predisposition", "Cancer Predisposition", "Hereditary Neoplastic Syndrome", "Hereditary Neoplastic Syndrome" ], "keyword": "Hereditary cancer syndrome" } ], "review_date": 20211105, "review_description": "Likely pathogenic", "title": "NM_000546.6(TP53):c.487T>A (p.Tyr163Asn) AND Hereditary cancer-predisposing syndrome", "review_status": "criteria provided, single submitter", "submission_description": [], "submissions": [ { "submitter_name": "Ambry Genetics", "submission_description": [ "The p.Y163N variant (also known as c.487T>A), located in coding exon 4 of the TP53 gene, results from a T to A substitution at nucleotide position 487. The tyrosine at codon 163 is replaced by asparagine, an amino acid with dissimilar properties. This variant is in the DNA binding domain of the TP53 protein and is reported to have non-functional transactivation in yeast based assays (Kato S et al. Proc. Natl. Acad. Sci. USA. 2003 Jul;100:8424-9). Studies conducted in human cell lines indicate this alteration is deficient at growth suppression and has a dominant negative effect (Kotler E et al. Mol.Cell. 2018 Jul;71:178-190.e8; Giacomelli AO et al. Nat. Genet. 2018 Oct;50:1381-1387). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic." ], "review_status": "criteria provided, single submitter", "submitter_date": 20240424, "review_description": "Likely pathogenic", "method": "clinical testing", "review_date": 20211105, "origin": "germline", "diseases": [ { "symbols": { "medgen": "C0027672" } } ], "date_updated": 20240501, "clinical_significance": [ "Likely pathogenic" ], "accession_id": "SCV002638731" } ], "variant_id": 10190170075784430004 }, { "variation_id": 376679, "accession_id": "RCV000633347", "clinical_significance": [ "Uncertain significance" ], "allele_id": 363558, "date_created": 20180528, "review_stars": 1, "diseases": [ { "normalized_disease": [ "Li-Fraumeni Syndrome" ], "normalized_cancer": [ "Sarcoma family syndrome of Li and Fraumeni" ], "symbols": { "omim": "151623", "medgen": "C0085390", "mondo": "MONDO:0018875" }, "pub_med": [ 17392385, 24493721, 26389210, 26389258 ], "names": [ "Li-Fraumeni Syndrome", "Sarcoma Family Syndrome Li Fraumeni" ] } ], "review_date": 20170824, "review_description": "Uncertain significance", "title": "NM_000546.6(TP53):c.487T>A (p.Tyr163Asn) AND Li-Fraumeni syndrome", "review_status": "criteria provided, single submitter", "submission_description": [], "submissions": [ { "submitter_name": "Invitae", "submission_description": [ "In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. A different missense substitution at this codon (p.Tyr163Cys) has been determined to be pathogenic (Invitae). This suggests that the tyrosine residue is critical for TP53 protein function and that other missense substitutions at this position may also be pathogenic. Experimental studies in yeast have shown that this missense change disrupts TP53 transactivation activity (PMID:¬†12826609). This variant has not been reported in the literature in individuals with TP53-related disease. ClinVar contains an entry for this variant (Variation ID: 376679). This variant is not present in population databases (ExAC no frequency). This sequence change replaces tyrosine with asparagine at codon 163 of the TP53 protein (p.Tyr163Asn). The tyrosine residue is highly conserved and there is a large physicochemical difference between tyrosine and asparagine." ], "review_status": "criteria provided, single submitter", "submitter_date": 20240208, "review_description": "Uncertain significance", "method": "clinical testing", "review_date": 20170824, "origin": "germline", "diseases": [ { "symbols": { "medgen": "C0085390" } } ], "date_updated": 20240214, "clinical_significance": [ "Uncertain significance" ], "accession_id": "SCV000754569" } ], "variant_id": 10190170075784430004 }, { "variation_id": 376679, "accession_id": "RCV000437297", "clinical_significance": [ "Likely pathogenic" ], "allele_id": 363558, "date_created": 20170308, "review_stars": 0, "diseases": [ { "normalized_disease": [ "Lung Adenocarcinoma", "Lung Cancer" ], "normalized_cancer": [ "Lung Adenocarcinoma In Situ" ], "symbols": { "medgen": "C0152013", "mesh": "D000077192", "mondo": "MONDO:0005061", "human_phenotype_ontology": "HP:0030078" }, "pub_med": [ 23562183, 25311215, 24627688, 29355391, 29398453 ], "names": [ "Lung Adenocarcinoma", "Lung Adenocarcinoma", "Lung Cancer" ] } ], "review_date": 20160531, "review_description": "Likely pathogenic", "title": "NM_000546.6(TP53):c.487T>A (p.Tyr163Asn) AND Lung adenocarcinoma", "review_status": "no assertion criteria provided", "submission_description": [], "submissions": [ { "submitter_name": "Database of Curated Mutations (DoCM)", "submission_description": [], "review_status": "no assertion criteria provided", "submitter_date": 20160718, "review_description": "Likely pathogenic", "method": "literature only", "review_date": 20160531, "origin": "somatic", "diseases": [ { "symbols": { "mesh": "C538231" } } ], "date_updated": 20170308, "clinical_significance": [ "Likely pathogenic" ], "accession_id": "SCV000510082" } ], "variant_id": 10190170075784430004 }, { "variation_id": 376679, "accession_id": "RCV000443298", "clinical_significance": [ "Likely pathogenic" ], "allele_id": 363558, "date_created": 20170308, "review_stars": 0, "diseases": [ { "normalized_disease": [ "Head and Neck Squamous Cell Carcinoma" ], "normalized_cancer": [ "Head and Neck Squamous Cell Carcinoma" ], "symbols": { "orphanet": "67037", "omim": "275355", "medgen": "C1168401", "mesh": "D000077195", "mondo": "MONDO:0010150" }, "names": [ "Head and Neck Squamous Cell Carcinoma", "Head and Neck Squamous Cell Carcinoma", "Head and Neck Squamous Cell Carcinoma", "Head and Neck Squamous Cell Carcinoma" ], "keyword": "Hereditary cancer syndrome" } ], "review_date": 20160531, "review_description": "Likely pathogenic", "title": "NM_000546.6(TP53):c.487T>A (p.Tyr163Asn) AND Squamous cell carcinoma of the head and neck", "review_status": "no assertion criteria provided", "submission_description": [], "submissions": [ { "submitter_name": "Database of Curated Mutations (DoCM)", "submission_description": [], "review_status": "no assertion criteria provided", "submitter_date": 20160718, "review_description": 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[ { "type": "variant", "id": "10190170075784430004", "count": 23 }, { "type": "gene", "id": 33956, "count": 54709, "symbol": "TP53" } ], "uniprot_variants": [ { "version": "03-Jun-2024", "items": [ { "annotation_id": "VAR_044871", "protein_id": "E7EMR6", "proteinname": "Cellular tumor antigen p53 (Fragment)", "somaticstatus": "False", "frequency": null, "gene": "TP53", "clinicalsignificances": [ "Likely pathogenic", "Unclassified" ], "transcripts": null, "association": [ { "disease": "Breast neoplasm", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Carcinoma of esophagus", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Hepatocellular carcinoma ", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Hereditary cancer-predisposing syndrome", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Li-Fraumeni syndrome ", "disease_description": "Li-Fraumeni syndrome (LFS) is a cancer predisposition syndrome associated with high risks for a diverse spectrum of childhood- and adult-onset malignancies.", "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Lung adenocarcinoma", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Malignant melanoma of skin ", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": { "pub_med_references": [ 33651321 ], "cosmic_study": null } }, { "disease": "Neoplasm of brain", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Neoplasm of the large intestine", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Ovarian serous cystadenocarcinoma", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Pancreatic adenocarcinoma", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Small cell lung carcinoma", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Squamous cell carcinoma of the head and neck ", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Squamous cell lung carcinoma", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} }, { "disease": "Uterine carcinosarcoma", "disease_description": null, "disease_symbol": null, "disease_alt_symbol": null, "evidences": {} } ], "siftscore": null, "siftprediction": null, "polyphenscore": null, "polyphenprediction": null, "evidences": { "pub_med_references": [ 8509216, 8655704, 8826941, 9288052, 9796697, 10091733, 10589767, 10998080, 11358811, 15956964, 17410283, 22634756 ], "cosmic_study": [ "323", "331", "403", "582" ] }, "xrefs": { "cosmicmutationid": [ "COSM307267", "COSM307268", "COSM3717661", "COSM3717662", "COSM44623" ], "clinvaraccession": [] }, "variant_type": "Unclassified", "disease": "Breast neoplasm", "disease_symbol": null, "disease_alt_symbol": null, "bed_comments": null, "pub_med_references": [ 8509216, 8655704, 8826941, 9288052, 9796697, 10091733, 10589767, 10998080, 11358811, 15956964, 17410283, 22634756 ] } ] } ], "nih_gdc": [ { "version": "08-Dec-2023", "sex": [ { "key": "Female", "value": 1 } ], "age_freq": [ { "key": "50-60", "value": 1 } ], "os_status": [ { "key": "Living", "value": 1 } ], "race": [ { "key": "European (non-Finnish)", "value": 1 } ], "tumor_status": null, "tumor_tissue_site": null, "path_t_stage": null, "path_n_stage": null, "path_m_stage": null, "clin_t_stage": null, "clin_n_stage": null, "clin_m_stage": null, "ajcc_pathologic_tumor_stage": null, "total_samples": 3, "study_name": null, "prior_dx": null, "drug": null, "measure_of_response": null, "therapy_type": [ { "key": "Chemotherapy", "value": 6 } ], "route_of_administration": [ { "key": "Iv", "value": 5 }, { "key": "Ip", "value": 1 } ], "therapy_ongoing": [ { "key": "NO", "value": 6 } ], "clinical_significance": [ { "key": "Likely Pathogenic", "value": 3 }, { "key": "Uncertain Significance", "value": 3 } ], "pub_med_references": null, "oncotree_code": [ { "key": "OVARY", "value": 1 } ], "cancer_name": [ { "key": "Serous Cystadenocarcinoma", "value": 1 } ], "cancer_type": [ { "key": "Ovarian/Fallopian Tube Cancer, NOS", "value": 1 } ], "tissue_type": [ { "key": "Ovary/Fallopian Tube", "value": 1 } ] } ], "saphetor_known_pathogenicity": [ { "version": "05-Aug-2024", "items": [ { "annotations": { "NCBI ClinVar2": [ { "functions": [ "coding" ], "coding_impact": "missense", "acmg_confirmed": false, "acmg_class": "Uncertain Significance", "acmg_reannotated": "Pathogenic", "source": "NCBI ClinVar2", "codon": 163, "gene_symbol": "TP53", "hgvs": "Y163N", "transcript": "ENST00000269305.4", "submission_count": 17, "review_stars": 1, "accession_count": 17, "publication_count": 1, "clinical_significance": [ "conflicting interpretations of pathogenicity" ], "pub_med_references": [ 10229196 ], "disease_name": [ "Adult Hepatocellular Carcinoma", "Brain Neoplasm", "Breast Neoplasm", "Breast Neoplasms", "Cancer Predisposition" ], "is_conflicting": true, "submissions_b": 0, "submissions_p": 16, "submissions_vus": 1 } ], "UNIPROT UniProt Variants": [ { "functions": [ "coding" ], "coding_impact": "missense", "acmg_confirmed": false, "acmg_class": "Uncertain Significance", "acmg_reannotated": "Pathogenic", "source": "UNIPROT UniProt Variants", "codon": 163, "gene_symbol": "TP53", "hgvs": "Y163N", "transcript": "ENST00000269305.4", "possible_functional_studies": [ 8826941 ], "pub_med_references": [ 8826941, 9288052, 9796697, 10091733, 10589767, 10998080, 11358811, 15956964, 17410283, 22634756 ], "disease_name": [ "Breast neoplasm", "Carcinoma of esophagus", "Hepatocellular carcinoma", "Hereditary cancer-predisposing syndrome", "Li-Fraumeni syndrome" ], "annotation_id": "VAR_044871" } ] } } ] } ], "acmg_annotation": { "version_name": "12.1.1", "gene_symbol": "TP53", "transcript": "ENST00000269305.4", "transcript_reason": "MANE select", "coding_impact": "missense", "blosum_score": -5, "verdict": { "ACMG_rules": { "benign_score": 0, "benign_subscore": "Uncertain Significance", "clinical_score": 5.2620000000000005, "pathogenic_score": 12, "pathogenic_subscore": "Pathogenic", "total_score": 12, "verdict": "Pathogenic" }, "classifications": [ "PM1_Strong", "PP3_Strong", "PM5", "PM2_Supporting", "PP5" ] }, "classifications": [ { "name": "PM1", "met_criteria": true, "user_explain": [ "Hot-spot of length 17 amino-acids has 104 missense/in-frame variants (31 pathogenic variants, 73 uncertain variants and no benign), which qualifies as strong pathogenic.", "UniProt protein P53_HUMAN region of interest 'Required for interaction with FBXO42' has 665 missense/in-frame variants (218 pathogenic variants, 441 uncertain variants and 6 benign variants), which qualifies as moderate pathogenic.", "UniProt protein P53_HUMAN DNA-binding domain 'DNA-binding region_102-292' has 1 084 missense/in-frame variants (419 pathogenic variants, 657 uncertain variants and 8 benign variants), which qualifies as moderate pathogenic.", "UniProt protein P53_HUMAN region of interest 'Interaction with AXIN1' has 1 014 missense/in-frame variants (392 pathogenic variants, 615 uncertain variants and 7 benign variants), which qualifies as moderate pathogenic.", "UniProt protein P53_HUMAN region of interest 'Required for interaction with ZNF385A' has 1 112 missense/in-frame variants (420 pathogenic variants, 684 uncertain variants and 8 benign variants), which qualifies as moderate pathogenic.", "UniProt protein P53_HUMAN region of interest 'Interaction with HIPK1' has 1 382 missense/in-frame variants (453 pathogenic variants, 885 uncertain variants and 44 benign variants), which qualifies as moderate pathogenic.", "UniProt protein P53_HUMAN region of interest 'Interaction with CCAR2' has 1 469 missense/in-frame variants (436 pathogenic variants, 991 uncertain variants and 42 benign variants), which qualifies as supporting pathogenic." ], "strength": "Strong" }, { "name": "PP3", "met_criteria": true, "user_explain": [ "MetaRNN = 0.988 is greater than 0.939 ⇒ strong pathogenic." ], "strength": "Strong" }, { "name": "PM5", "met_criteria": true, "user_explain": [ "Alternative variant ##chr17:7578442 T⇒C## (Tyr163Cys) is classified Pathogenic by UniProt Variants (confirmed using the germline classifier)." ] }, { "name": "PM2", "met_criteria": true, "user_explain": [ "Variant not found in gnomAD genomes, good gnomAD genomes coverage = 31.9.", "Variant not found in gnomAD exomes, good gnomAD exomes coverage = 88.3." ], "strength": "Supporting" }, { "name": "PP5", "met_criteria": true, "user_explain": [ "Combined evidence strength is Supporting (score = 1).", "Supporting: ClinVar classifies this variant as Uncertain Significance but a high confidence submitter has classified as Likely Pathogenic, 1 star (reviewed Jun '24, 17 submissions of which 1 is from high confidence submitter), citing %%PUBMED:10229196%%, associated with Breast Neoplasm." ] } ], "gene_id": 33956, "sample_findings": { "phenotypes": "No matching phenotype found for gene TP53 which is associated with Adrenal Cortex Carcinoma, Adrenal Cortical Carcinoma, 202300, Adrenal, Breast, Brain, And Lung Sarcoma, Gastrointestinal Cancers, Breast Cancer, Osteosarcoma, Soft Tissue Sarcomas, Brain Tumors, Adrenocortical Carcinoma, Adrenocortical Carcinoma, Hereditary and 40 more, according to CGD, ClinGen Disease Validity, GenCC, Mondo, PanelApp and gene2phenotype.", "mode_of_inheritance": "AD, based on gene information from CGD, ClinGen Disease Validity, GenCC, Mondo, PanelApp and gene2phenotype." } }, "amp_annotation": { "version_name": "12.1.1", "verdict": { "tier": "Tier II", "approx_score": 2.3249999999999997 }, "classifications": [ { "name": "Crtd", "tier": "Tier II", "user_explain": { "Tier II": [ "DoCM reports 14 entries classified Tier II citing %%PUBMED:26619011%% related to the following 13 cancers: Bowel, Breast, CNS/Brain, Esophagus/Stomach, Head and Neck Squamous Cell Carcinoma and 8 more." ] }, "approx_score": 3.2 }, { "name": "Drug", "tier": "Tier II", "user_explain": { "Tier II": [ "Cisplatin, Etoposide and Mitomycin (curated), reported by CIViC, related to Esophagus/Stomach - but no patient cancer type was provided for matching.", "Doxorubicin and Tamoxifen (curated), reported by CIViC, related to Breast - but no patient cancer type was provided for matching.", "Docetaxel and Docetaxel, Selumetinib (curated), reported by CIViC, related to Lung - but no patient cancer type was provided for matching.", "Pazopanib and Vorinostat (curated), reported by CIViC, related to Solid Tumor - but no patient cancer type was provided for matching.", "Capecitabine, Cetuximab, Oxaliplatin (curated), reported by CIViC, related to Bowel - but no patient cancer type was provided for matching.", "Carboplatin, Cisplatin (curated), reported by CIViC, related to Ovary/Fallopian Tube - but no patient cancer type was provided for matching." ] }, "approx_score": 5.0 }, { "name": "Germ", "tier": "Tier I", "user_explain": { "Tier I": [ "This variant is classified Pathogenic, by the germline classifier rules PM1_Strong, PP3_Strong, PM5, PM2_Supporting and PP5." ] }, "approx_score": 3.1 }, { "name": "Soma", "tier": "Tier I", "user_explain": { "Tier I": [ "This variant is reported in 68 out of the 42 872 somatic samples for gene TP53, which has 5 872 reported somatic variants. It is not found in GnomAD. This is statistically rated Tier I." ] }, "total_samples": 68, "approx_score": 2.0 }, { "name": "Pubs", "tier": "Tier III", "approx_score": 3.0 }, { "name": "Path", "tier": "Tier I", "user_explain": { "Tier I": [ "The Human Protein Atlas classifies TP53 as tumour-suppressing." ], "Tier II": [ "BioCarta associates gene TP53 with the following 4 cancers: Breast, RB Tumor Suppressor/Checkpoint Signaling in response to DNA damage, Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility and Tumor Suppressor Arf Inhibits Ribosomal Biogenesis.", "Consensus associates gene TP53 with the following 31 cancers: Adenoid Cystic Carcinoma, Basal Cell Carcinoma, Bladder/Urinary Tract, Breast, CNS/Brain and 26 more.", "GHR reports that the TP53 gene provides instructions for making a protein called tumor protein p53 (or p53). Also, associates TP53 with the following 9 cancers: Bladder/Urinary Tract, Breast, Cholangiocarcinoma, Head and Neck Squamous Cell Carcinoma, Li-Fraumeni Syndrome and 4 more.", "KEGG reports that gene TP53 is involved in MAPK signaling pathway, Wnt signaling pathway and p53 signaling pathway. Also, associates TP53 with the following 12 cancers: Basal Cell Carcinoma, Bladder/Urinary Tract, Colorectal cancer, Endometrial cancer, Glioma and 7 more.", "Mondo associates gene TP53 with the following 9 cancers: B-Cell Chronic Lymphocytic Leukemia, Bone Osteosarcoma, Choroid Plexus Carcinoma, Choroid Plexus Papilloma, Hepatocellular Carcinoma and 4 more." ] }, "approx_score": 4.0 }, { "name": "Type", "tier": "Tier III", "user_explain": { "Tier III": [ "ACMG rule PVS1 did not trigger.", "ACMG rule PM4 did not trigger.", "Variant is not predicted splicing: no prediction from MaxEntScan." ] }, "approx_score": 2.0 }, { "name": "Freq", "tier": "Tier II", "user_explain": { "Tier II": [ "ACMG rule PM2 was triggered with strength Supporting: Variant not found in gnomAD genomes, good gnomAD genomes coverage = 31.9.\nVariant not found in gnomAD exomes, good gnomAD exomes coverage = 88.3." ] }, "approx_score": 2.0 }, { "name": "Pred", "tier": "Tier III", "user_explain": { "Tier III": [ "Uncertain Significance computational verdict based on 1 pathogenic prediction from MetaRNN, conflicting with no benign predictions (and 1 uncertain prediction from DANN)." ] }, "approx_score": 1.0 } ] }, "cbio_portal": [ { "version": "06-Jun-2023", "total_samples": 31, "sample_id": null, "sample_type": [ { "key": "Primary", "value": 17 }, { "key": "Metastasis", "value": 7 }, { "key": "Metastatic", "value": 1 } ], "study_name": null, "mutation_status": [ { "key": "Somatic", "value": 16 } ], "validation_status": [ { "key": "Valid", "value": 4 } ], "center": [ { "key": "Mskcc", "value": 11 }, { "key": "Broad.Mit.Edu", "value": 2 }, { "key": "Fhcrc", "value": 2 }, { "key": "Genome.Wustl.Edu", "value": 2 }, { "key": "Bgi", "value": 1 }, { "key": "Inserm.Fr", "value": 1 }, { "key": "Mdanderson.Org/Ucsc.Edu/Broad.Mit.Edu", "value": 1 }, { "key": "Msk-Impact410", "value": 1 }, { "key": "Riken", "value": 1 } ], "t_ref_count": 4404, "t_alt_count": 3928, "n_ref_count": 6881, "n_alt_count": 2, "n_depth": 415, "t_depth": 318, "canonical": true, "hotspot": false, "ensp": "ENSP00000269305", "ccds": "CCDS11118.1", "cdsposition": "487", "cdnaposition": "677", "biotype": "Protein_Coding", "uniparc": "UPI000002ED67", "pick": 1.0, "sex": [ { "key": "Male", "value": 18 }, { "key": "Female", "value": 11 } ], "age_freq": [ { "key": "50-60", "value": 6 }, { "key": "30-40", "value": 5 }, { "key": "70-80", "value": 3 } ], "os_months": [ { "key": "11", "value": 3 }, { "key": "13", "value": 3 }, { "key": "7", "value": 2 }, { "key": "77", "value": 2 }, { "key": "15", "value": 1 }, { "key": "16", "value": 1 }, { "key": "2", "value": 1 }, { "key": "3", "value": 1 }, { "key": "33", "value": 1 }, { "key": "35", "value": 1 }, { "key": "47", "value": 1 }, { "key": "9", "value": 1 } ], "os_status": [ { "key": "Living", "value": 13 }, { "key": "Deceased", "value": 8 } ], "race": [ { "key": "European (non-Finnish)", "value": 10 } ], "tumor_status": [ { "key": "Recurred", "value": 4 } ], "dfs_months": [ { "key": "55", "value": 2 }, { "key": "10", "value": 1 }, { "key": "7", "value": 1 } ], "path_t_stage": null, "pfs_status": [ { "key": "Yes", "value": 3 }, { "key": "No", "value": 1 } ], "radiation_therapy": [ { "key": "Yes", "value": 2 }, { "key": "No", "value": 1 } ], "path_n_stage": null, "path_m_stage": null, "new_tumor_event_after_initial_treatment": [ { "key": "No", "value": 1 }, { "key": "YES", "value": 1 }, { "key": "Yes", "value": 1 } ], "ajcc_pathologic_tumor_stage": null, "dss_status": [ { "key": "0:Alive Or Dead Tumor Free", "value": 2 }, { "key": "1.0", "value": 1 }, { "key": "1:Dead With Tumor", "value": 1 } ], "prior_dx": [ { "key": "No", "value": 2 } ], "somatic_status_freq": [ { "key": "Yes", "value": 23 } ], "grade": [ { "key": "G2", "value": 3 }, { "key": "G3", "value": 2 } ], "pub_med_references": null, "oncotree_code": [ { "key": "HCC", "value": 6 }, { "key": "PRAD", "value": 6 }, { "key": "LUAD", "value": 4 }, { "key": "MPNST", "value": 3 }, { "key": "DIFG", "value": 2 }, { "key": "SOC", "value": 2 }, { "key": "CHL", "value": 1 }, { "key": "ESCA", "value": 1 }, { "key": "ESCC", "value": 1 }, { "key": "GBM", "value": 1 }, { "key": "HGSOC", "value": 1 }, { "key": "MEL", "value": 1 }, { "key": "PANCREAS", "value": 1 }, { "key": "USC", "value": 1 } ], "cancer_name": [ { "key": "Hepatobiliary Cancer", "value": 6 }, { "key": "Prostate Cancer", "value": 6 }, { "key": "Non-Small Cell Lung Cancer", "value": 4 }, { "key": "Glioma", "value": 3 }, { "key": "Esophagogastric Cancer", "value": 2 }, { "key": "Nerve Sheath Tumor", "value": 2 }, { "key": "Ovarian Cancer", "value": 2 }, { "key": "Endometrial Cancer", "value": 1 }, { "key": "Hodgkin Lymphoma", "value": 1 }, { "key": "Melanoma", "value": 1 }, { "key": "Ovarian Epithelial Tumor", "value": 1 }, { "key": "Pancreatic Cancer", "value": 1 }, { "key": "Sarcoma", "value": 1 } ], "cancer_type": [ { "key": "Hepatobiliary Cancer", "value": 6 }, { "key": "Prostate Cancer", "value": 6 }, { "key": "Non-Small Cell Lung Cancer", "value": 4 }, { "key": "Glioma", "value": 3 }, { "key": "Nerve Sheath Tumor", "value": 3 }, { "key": "Ovarian Cancer", "value": 3 }, { "key": "Esophagogastric Cancer", "value": 2 }, { "key": "Endometrial Cancer", "value": 1 }, { "key": "Hodgkin Lymphoma", "value": 1 }, { "key": "Melanoma", "value": 1 }, { "key": "Pancreatic Cancer, NOS", "value": 1 } ], "tissue_type": [ { "key": "Liver", "value": 6 }, { "key": "Prostate", "value": 6 }, { "key": "Lung", "value": 4 }, { "key": "CNS/Brain", "value": 3 }, { "key": "Ovary/Fallopian Tube", "value": 3 }, { "key": "Peripheral Nervous System", "value": 3 }, { "key": "Esophagus/Stomach", "value": 2 }, { "key": "Lymphoid", "value": 1 }, { "key": "Pancreas", "value": 1 }, { "key": "Skin", "value": 1 }, { "key": "Uterus", "value": 1 } ] } ], "cancer_hotspots": [ { "version": "10-Sep-2021", "total_samples": 9, "t_ref_count": 381, "t_alt_count": 374, "n_ref_count": null, "n_alt_count": null, "n_depth": 0, "t_depth": 1678, "somatic": null, "canonical": true, "ensp": "ENSP00000269305", "ccds": "CCDS11118.1", "cdsposition": "487/1182", "cdnaposition": "677/2579", "biotype": "protein_coding", "feature": "ENST00000269305", "uniparc": "Upi000002Ed67", "pick": 1.0, "pub_med_references": null, "oncotree_code": [ { "key": "HCC", "value": 3 }, { "key": "CHL", "value": 1 }, { "key": "ESCA", "value": 1 }, { "key": "LGGNOS", "value": 1 }, { "key": "LUAD", "value": 1 }, { "key": "SOC", "value": 1 } ], "cancer_name": [ { "key": "Hepatocellular Carcinoma", "value": 3 }, { "key": "Classical Hodgkin Lymphoma", "value": 1 }, { "key": "Esophageal Adenocarcinoma", "value": 1 }, { "key": "Low-Grade Glioma, NOS", "value": 1 }, { "key": "Lung Adenocarcinoma", "value": 1 }, { "key": "Serous Ovarian Cancer", "value": 1 } ], "cancer_type": [ { "key": "Hepatobiliary Cancer", "value": 3 }, { "key": "Esophagogastric Cancer", "value": 1 }, { "key": "Glioma", "value": 1 }, { "key": "Hodgkin Lymphoma", "value": 1 }, { "key": "Non-Small Cell Lung Cancer", "value": 1 }, { "key": "Ovarian Cancer", "value": 1 } ], "tissue_type": [ { "key": "Liver", "value": 3 }, { "key": "CNS/Brain", "value": 1 }, { "key": "Esophagus/Stomach", "value": 1 }, { "key": "Lung", "value": 1 }, { "key": "Lymphoid", "value": 1 }, { "key": "Ovary/Fallopian Tube", "value": 1 } ] } ], "phylop100way": [ { "version": "13-Apr-2021", "conservation_score": [ "9.291" ] } ], "maxentscan": null, "wustl_docm": [ { "version": "07-Jun-2022", "diseases": [ { "disease": "lung adenocarcinoma", "doid": "3910", "tags": [ "likely pathogenic" ] }, { "disease": "esophageal carcinoma", "doid": "1107", "tags": [ "likely pathogenic" ] }, { "disease": "brain stem glioma", "doid": "4202", "tags": [ "likely pathogenic" ] }, { "disease": "head and neck squamous cell carcinoma", "doid": "5520", "tags": [ "likely pathogenic" ] }, { "disease": "ovarian serous cystadenocarcinoma", "doid": "5746", "tags": [ "likely pathogenic" ] }, { "disease": "uterine carcinosarcoma", "doid": "6171", "tags": [ "likely pathogenic" ] }, { "disease": "skin melanoma", "doid": "8923", "tags": [ "likely pathogenic" ] }, { "disease": "pancreas adenocarcinoma", "doid": "4074", "tags": [ "likely pathogenic" ] }, { "disease": "brain glioma", "doid": "0060108", "tags": [ "likely pathogenic" ] }, { "disease": "hepatocellular carcinoma", "doid": "684", "tags": [ "likely pathogenic" ] }, { "disease": "lung small cell carcinoma", "doid": "5409", "tags": [ "likely pathogenic" ] }, { "disease": "breast cancer", "doid": "1612", "tags": [ "likely pathogenic" ] }, { "disease": "lung squamous cell carcinoma", "doid": "3907", "tags": [ "likely pathogenic" ] }, { "disease": "colorectal cancer", "doid": "9256", "tags": [ "likely pathogenic" ] } ], "drugs": null, "pub_med_references": null, "hgvs": "ENST00000269305:c.487T>A" } ] }