{ "data": { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/13918561-f552-46bc-a22c-f090b5a93152/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 1.5", "type": "VariantPathogenicityInterpretationGuideline", "version": "1.5" }, "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/CA16619259/MONDO:0700270/020/el/0/1798", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA16619259/MONDO:0700270/020/ei/1/1799", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "contributionDate": { "date": "2026/8/5", "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/CA16619259/MONDO:0700270/020/el/0/1798/1800", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA16619259/MONDO:0700270/020/ci/CA16619259/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 population minor allele frequency in gnomAD v4 is 0.000016 (1/60002 alleles) in Admixed American population which is higher than the ClinGen HBOP threshold 0.001% for PM2_Supporting", "contributionDate": { "date": "2026/8/5", "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": "CA16619259/MONDO:0700270/020/ci/CA16619259/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/0/1798/1800", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/1/1799", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/0/1798", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA16619259/MONDO:0700270/020/el/0/1678", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA16619259/MONDO:0700270/020/ei/1/1679", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "contributionDate": { "date": "2026/8/5", "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/CA16619259/MONDO:0700270/020/el/0/1678/1680", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA16619259/MONDO:0700270/020/ci/CA16619259/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 reported to segregate with Ataxia-Telangiectasia in two affected individuals from one family (personal communication)", "contributionDate": { "date": "2026/8/5", "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": "CA16619259/MONDO:0700270/020/ci/CA16619259/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/0/1678/1680", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/1/1679", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/0/1678", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA16619259/MONDO:0700270/020/el/0/1747", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA16619259/MONDO:0700270/020/ei/1/1748", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "contributionDate": { "date": "2026/8/5", "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/CA16619259/MONDO:0700270/020/el/0/1747/1749", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA16619259/MONDO:0700270/020/ci/CA16619259/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 computational predictor REVEL gives a score of 0.952, which is above the threshold of 0.733, evidence that correlates with impact to ATM function (PP3). \n\nSpliceAI does not predict any aberrant splicing associated with this variant. ", "contributionDate": { "date": "2026/8/5", "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": "CA16619259/MONDO:0700270/020/ci/CA16619259/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/0/1747/1749", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/1/1748", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/0/1747", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA16619259/MONDO:0700270/020/el/0/1651", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA16619259/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": "2026/8/5", "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/CA16619259/MONDO:0700270/020/el/0/1651/1653", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA16619259/MONDO:0700270/020/ci/CA16619259/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 3 individuals with Ataxia-Telangiectasia. Of those individuals, two were confirmed in trans by family testing (personal communication). One individual was homozygous for the variant (PMID: 9711876; PMID: 37438524)(PM3_Strong).", "contributionDate": { "date": "2026/8/5", "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": "CA16619259/MONDO:0700270/020/ci/CA16619259/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/0/1651/1653", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/1/1652", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020/0/1651", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA16619259/MONDO:0700270/020", "metadata": { "created": "2026-08-05T19:04:40.122Z", "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": "Wed, 05 Aug 2026 19:04:40 -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": "13918561-f552-46bc-a22c-f090b5a93152", "variant": { "@id": "https://reg.genome.network/allele/CA16619259", "id": "CAR:CA16619259", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000051.4:c.8486C>T" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000051.4(ATM):c.8486C>T (p.Pro2829Leu)" } ], "type": "CAR" } }, "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-10-29T02:04:12.860Z" } }, "status": { "code": 200, "name": "OK" } }