{ "data": { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/cf42b25c-cac5-48e0-b3ca-83407767b8bb/doc/sepio/version/1.1.0", "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 1.4.0", "type": "VariantPathogenicityInterpretationGuideline", "version": "1.4.0" }, "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/CA382561906/MONDO:0700270/020/el/0/1594", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA382561906/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": "2026/8/5", "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/CA382561906/MONDO:0700270/020/el/0/1594/1596", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA382561906/MONDO:0700270/020/ci/CA382561906/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 leads to partial skipping of exon 54 (Ambry internal data), PVS1 (RNA)", "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": "CA382561906/MONDO:0700270/020/ci/CA382561906/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/0/1594/1596", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/1/1595", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/0/1594", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA382561906/MONDO:0700270/020/el/0/1747", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA382561906/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/CA382561906/MONDO:0700270/020/el/0/1747/1749", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA382561906/MONDO:0700270/020/ci/CA382561906/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": "Applying PVS1[RNA]\nThe computational splicing predictor SpliceAI gives a score of 0.97 for donor gain, predicting that the variant disrupts the donor splice site of ATM. ", "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": "CA382561906/MONDO:0700270/020/ci/CA382561906/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/0/1747/1749", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/1/1748", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/0/1747", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA382561906/MONDO:0700270/020/el/0/1636", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA382561906/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": "2026/8/5", "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/CA382561906/MONDO:0700270/020/el/0/1636/1638", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA382561906/MONDO:0700270/020/ci/CA382561906/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 v4.1.0 is 0.0.00002229 (1/44868alleles) in East Asian population; while this is higher than the HBOP VCEP threshold ([≤0.00001]) for PM2_Supporting, it is present in only one allele, meeting this criterion. ", "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": "CA382561906/MONDO:0700270/020/ci/CA382561906/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/0/1636/1638", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/1/1637", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/0/1636", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA382561906/MONDO:0700270/020/el/0/1609", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA382561906/MONDO:0700270/020/ei/1/1610", "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/CA382561906/MONDO:0700270/020/el/0/1609/1611", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA382561906/MONDO:0700270/020/ci/CA382561906/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": "PMID: 12815592 This variant has been observed in an individual(In the list of variants detected from Iberian population(18 Hispanic-American families) with ataxia telangiectasia (A-T Patients) in Trans (Phased confirmed) with another ATM variant c.8150A>C (called LP by VCEP). \n*Of note, a clerical error previously listed that this variant co-occurred with c.8150T>G. \n", "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": "CA382561906/MONDO:0700270/020/ci/CA382561906/MONDO:0700270/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/0/1609/1611", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/1/1610", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020/0/1609", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA382561906/MONDO:0700270/020", "metadata": { "created": "2026-08-05T18:54:48.289Z", "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 18:54:48 -0000", "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)", "version": "1.1.0" }, "statementOutcome": { "@id": "https://loinc.org/LA6668-3", "id": "LN:LA6668-3", "label": "Pathogenic" }, "type": "VariantPathogenicityInterpretation", "uuid": "cf42b25c-cac5-48e0-b3ca-83407767b8bb", "variant": { "@id": "https://reg.genome.network/allele/CA382561906", "id": "CAR:CA382561906", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000051.4:c.8045C>G" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000051.4(ATM):c.8045C>G (p.Thr2682Ser)" } ], "type": "CAR" } }, "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-11-06T02:31:53.094Z" } }, "status": { "code": 200, "name": "OK" } }