{ "data": { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/cbf33d9d-4af0-4b9d-bc0d-163d4df14e20/doc/sepio/version/1.0.0", "assertionMethod": { "@id": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/135637581", "label": "ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.3.0", "type": "VariantPathogenicityInterpretationGuideline", "version": "2.3.0" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0018875", "id": "MONDO:0018875", "label": "Li-Fraumeni syndrome", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA497711354/MONDO:0018875/009/el/0/1678", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA497711354/MONDO:0018875/009/ei/1/1679", "contribution": [ { "agent": { "@id": 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Based on this evidence, this variant scores 2 total points meeting the TP53 VCEP phenotype scoring criteria of 2-3.5 points. (PS4_Moderate; Internal lab contributors).", "contributionDate": { "date": "2025/7/18", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA497711354/MONDO:0018875/009/ci/CA497711354/MONDO:0018875/009.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/0/1699/1701", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/1/1700", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/0/1699", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA497711354/MONDO:0018875/009/el/0/1612", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA497711354/MONDO:0018875/009/ei/1/1613", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50013_EP157989641412139", "id": "CG-PCER-AGENT:CG_50013_EP157989641412139", "type": "Agent" }, "contributionDate": { "date": "2025/7/18", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA497711354/MONDO:0018875/009/el/0/1612/1614", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA497711354/MONDO:0018875/009/ci/CA497711354/MONDO:0018875/009.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50013_EP157989641412139", "id": "CG-PCER-AGENT:CG_50013_EP157989641412139", "type": "Agent" }, "comments": "The NM_000546.6 c.1146del (p.Lys382AsnfsTer?) is a TP53 frameshift variant inducing a stop codon read-through. The variant is predicted to escape nonsense mediated decay, targeting a region of unknown function representing <10% of the protein and introducing a C-terminal extension of 28 residues in the protein (PVS1_Moderate).\n\nIt’s right at the end of the gene and predicted to cause a fs then a protein extension of 28 aa’s. Not predicted to be subject to NMD or NSD. Affects <10% of protein and not a functional domain although 3 of the aa’s affected are highly conserved but no pathogenic missense variants reported in this region.", "contributionDate": { "date": "2025/7/18", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA497711354/MONDO:0018875/009/ci/CA497711354/MONDO:0018875/009.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/0/1612/1614", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/1/1613", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/0/1612", "type": "EvidenceLine" }, { "@id": 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"CG-PCER-VARINT:CA497711354/MONDO:0018875/009/0/1804", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA497711354/MONDO:0018875/009/el/0/1588", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA497711354/MONDO:0018875/009/ei/1/1589", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50013_EP157989641412139", "id": "CG-PCER-AGENT:CG_50013_EP157989641412139", "type": "Agent" }, "contributionDate": { "date": "2025/7/18", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA497711354/MONDO:0018875/009/el/0/1588/1590", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA497711354/MONDO:0018875/009/ci/CA497711354/MONDO:0018875/009.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50013_EP157989641412139", "id": "CG-PCER-AGENT:CG_50013_EP157989641412139", "type": "Agent" }, "comments": "Additional functional studies are needed for code application (PS3/BS3 not met).", "contributionDate": { "date": "2025/7/18", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA497711354/MONDO:0018875/009/ci/CA497711354/MONDO:0018875/009.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/0/1588/1590", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/1/1589", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009/0/1588", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA497711354/MONDO:0018875/009", "metadata": { "created": "2025-07-18T20:00:53.764Z", "note": "DISCLAIMER: While the data/content in this document is approved by ClinGen expert panel(s), the SEPIO schema presented here is an initial prototype and has not been reviewed nor finalized by the ClinGen Data Exchange Modeling Team. We expect it to differ significantly from the final schema.", "producedAtUTC": "Fri, 18 Jul 2025 20:00:53 -0000", "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)", "version": "1.0.0" }, "statementOutcome": { "@id": "https://loinc.org/LA26332-9", "id": "LN:LA26332-9", "label": "Likely Pathogenic" }, "type": "VariantPathogenicityInterpretation", "uuid": "cbf33d9d-4af0-4b9d-bc0d-163d4df14e20", "variant": { "@id": "https://reg.genome.network/allele/CA497711354", "id": "CAR:CA497711354", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000546.6:c.1146del" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000546.6(TP53):c.1146del (p.Lys382fs)" } ], "type": "CAR" } }, "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-08-04T22:14:41.265Z" } }, "status": { "code": 200, "name": "OK" } }