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"https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0016419", "id": "MONDO:0016419", "label": "hereditary breast cancer", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1636", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/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": "2022/4/14", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0030", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0030", "label": "PM2", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1636/1638", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "comments": "Variant is absent in the GnomAD v2.1.1 cohort (PM2_Supporting).", "contributionDate": { "date": "2022/4/14", "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": "CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1636/1638", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/1/1637", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1636", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1651", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/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": "2022/4/14", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0058", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000330", "id": "SEPIO:0000330", "label": "Pathogenic Strong" }, "id": "0058", "label": "PM3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1651/1653", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "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 observed in a homozygous and/or compound heterozygous state (presumed and/or confirmed) in one/multiple individuals with Ataxia-Telangiectasia (PM3_Strong) (5 POINTS)", "contributionDate": { "date": "2022/4/14", "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": "CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1651/1653", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/1/1652", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1651", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1774", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/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": "2022/4/14", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0048", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0048", "label": "PM5", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1774/1776", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "comments": "In the absence of potential splicing rescue mechanisms in ATM, all PVS1-eligble truncating variants are expected to be pathogenic based on the existence of known pathogenic C-terminal truncations in the last exon (PM5_Supporting)", "contributionDate": { "date": "2022/4/14", "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": "CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1774/1776", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/1/1775", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1774", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1594", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/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": "2022/4/14", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0017", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000220", "id": "SEPIO:0000220", "label": "Pathogenic Very Strong" }, "id": "0017", "label": "PVS1", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1594/1596", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "comments": "Nonsense/Frameshift; NMD Prone", "contributionDate": { "date": "2022/4/14", "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": "CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1594/1596", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/1/1595", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1594", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020", "metadata": { "created": "2024-09-27T23:30:41.775Z", "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, 27 Sep 2024 23:30:41 -0000", "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)", "version": "1.2.0" }, "statementOutcome": { "@id": "https://loinc.org/LA6668-3", "id": "LN:LA6668-3", "label": "Pathogenic" }, "type": "VariantPathogenicityInterpretation", "uuid": "bf976c78-5c26-4e5b-bfcf-375b219c72be", "variant": { "@id": "https://reg.genome.network/allele/CA345709", "id": "CAR:CA345709", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000051.4:c.6997dup" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000051.4(ATM):c.6997dup" } ], "type": "CAR" } }, { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://erepo.genome.network/evrepo/api/summary/classification/bf976c78-5c26-4e5b-bfcf-375b219c72be/doc/sepio/version/1.1.0", "assertionMethod": { "type": "VariantPathogenicityInterpretationGuideline" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0016419", "id": "MONDO:0016419", "label": "hereditary breast cancer", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1636", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/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": "2022/3/16", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0030", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0030", "label": "PM2", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1636/1638", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "comments": "Variant is absent in the GnomAD v2.1.1 cohort (PM2_Supporting).", "contributionDate": { "date": "2022/3/16", "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": "CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1636/1638", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/1/1637", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1636", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1651", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/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": "2022/3/16", "description": "Date on which this evidence was 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individuals with Ataxia-Telangiectasia (PM3_Strong) (5 POINTS)", "contributionDate": { "date": "2022/3/16", "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": "CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1651/1653", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/1/1652", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1651", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1633", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/ei/1/1634", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50039_EP16468073603834", "id": "CG-PCER-AGENT:CG_50039_EP16468073603834", "type": "Agent" }, "contributionDate": { "date": "2022/3/16", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0063", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0063", "label": "PP4", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA345709/MONDO:0016419/020/el/0/1633/1635", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "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 was observed in a patient with Ataxia-Telangiectasia who lacked ATM protein expression (PMID 21459046-PP4)", "contributionDate": { "date": "2022/3/16", "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": "CA345709/MONDO:0016419/020/ci/CA345709/MONDO:0016419/020.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/0/1633/1635", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA345709/MONDO:0016419/020/1/1634", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" 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