{ "data": { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/347e9855-bece-4a30-ade8-c2f88b27b0ef/doc/sepio/version/1.0.0", "assertionMethod": { "@id": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/639508985", "label": "ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ATM Version 1.3.0", "type": "VariantPathogenicityInterpretationGuideline", "version": "1.3.0" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0700270", "id": "MONDO:0700270", "label": "ATM-related cancer predisposition", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA2695214771/MONDO:0700270/020/el/0/1651", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA2695214771/MONDO:0700270/020/ei/1/1652", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "contributionDate": { "date": "2026/4/10", "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/CA2695214771/MONDO:0700270/020/el/0/1651/1653", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA2695214771/MONDO:0700270/020/ci/CA2695214771/MONDO:0700270/020.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "comments": "This variant has been detected in at least 2 unrelated individuals with Ataxia-Telangiectasia (PMID: 26896183). ", "contributionDate": { "date": "2026/4/10", "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": "CA2695214771/MONDO:0700270/020/ci/CA2695214771/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/0/1651/1653", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/1/1652", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/0/1651", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA2695214771/MONDO:0700270/020/el/0/1774", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA2695214771/MONDO:0700270/020/ei/1/1775", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "contributionDate": { "date": "2026/4/10", "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/CA2695214771/MONDO:0700270/020/el/0/1774/1776", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA2695214771/MONDO:0700270/020/ci/CA2695214771/MONDO:0700270/020.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "comments": "This alteration results in a termination codon upstream of the most C-terminal pathogenic alteration (ATM p.Arg3047*), as classified by the HBOP VCEP, and is expected to be more deleterious (PM5_Supporting).\n", "contributionDate": { "date": "2026/4/10", "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": "CA2695214771/MONDO:0700270/020/ci/CA2695214771/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/0/1774/1776", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/1/1775", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/0/1774", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA2695214771/MONDO:0700270/020/el/0/1594", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA2695214771/MONDO:0700270/020/ei/1/1595", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "contributionDate": { "date": "2026/4/10", "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/CA2695214771/MONDO:0700270/020/el/0/1594/1596", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA2695214771/MONDO:0700270/020/ci/CA2695214771/MONDO:0700270/020.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "comments": "The c.4158dup (p.Lys1387Ter) (NM_000051.4) variant in ATM is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon leading to nonsense mediated decay (PVS1). \n", "contributionDate": { "date": "2026/4/10", "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": "CA2695214771/MONDO:0700270/020/ci/CA2695214771/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/0/1594/1596", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/1/1595", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/0/1594", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA2695214771/MONDO:0700270/020/el/0/1636", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA2695214771/MONDO:0700270/020/ei/1/1637", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "contributionDate": { "date": "2026/4/10", "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/CA2695214771/MONDO:0700270/020/el/0/1636/1638", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA2695214771/MONDO:0700270/020/ci/CA2695214771/MONDO:0700270/020.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "comments": "The highest minor allele frequency in gnomAD v4.1.0 is 0.00003381 (1/29576 alleles) in Ashkenazi Jewish population, which is higher than the ClinGen HBOP VCEP threshold (>.001%, N=1) for PM2_Supporting, meeting this criterion (PM2_Supporting). \n", "contributionDate": { "date": "2026/4/10", "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": "CA2695214771/MONDO:0700270/020/ci/CA2695214771/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/0/1636/1638", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/1/1637", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020/0/1636", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA2695214771/MONDO:0700270/020", "metadata": { "created": "2026-04-10T19:19:40.239Z", "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, 10 Apr 2026 19:19:40 -0000", "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)", "version": "1.0.0" }, "statementOutcome": { "@id": "https://loinc.org/LA6668-3", "id": "LN:LA6668-3", "label": "Pathogenic" }, "type": "VariantPathogenicityInterpretation", "uuid": "347e9855-bece-4a30-ade8-c2f88b27b0ef", "variant": { "@id": "https://reg.genome.network/allele/CA2695214771", "id": "CAR:CA2695214771", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000051.4:c.4158dup" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000051.4(ATM):c.4158dup (p.Lys1387Ter)" } ], "type": "CAR" } }, "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-11-05T10:01:08.573Z" } }, "status": { "code": 200, "name": "OK" } }