{ "data": [ { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://erepo.genome.network/evrepo/api/summary/classification/9e51dbad-5cbe-4a99-8a12-f7daf29fd7ab/doc/sepio/version/1.0.0", "assertionMethod": { "@id": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/135637580", "label": "ClinGen Myeloid Malignancy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2", "type": "VariantPathogenicityInterpretationGuideline", "url": "https://www.clinicalgenome.org/affiliation/50034/docs/assertion-criteria ", "version": "2.0.0" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0011071", "id": "MONDO:0011071", "label": "hereditary thrombocytopenia and hematologic cancer predisposition syndrome", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1774", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1775", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/CA410207974/MONDO:0011071/008/el/0/1774/1776", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "Two other missense variants (c.593A>T, p.Asp198Val, ClinVar Variation ID 627342 and c.592G>T (p.Asp198Tyr), CA410207975) in the same codon has been classified as likely pathogenic for Hereditary thrombocytopenia and hematologic cancer predisposition syndrome by the ClinGen MMVCEP (PM5_Supporting).", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1774/1776", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1775", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1774", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1672", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1673", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0010", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000216", "id": "SEPIO:0000216", "label": "Pathogenic Moderate" }, "id": "0010", "label": "PM6", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1672/1674", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "To our knowledge, no publication has reported this variant to date.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1672/1674", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1673", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1672", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1594", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1595", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/CA410207974/MONDO:0011071/008/el/0/1594/1596", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This is a missense variant.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1594/1596", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1595", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1594", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1678", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1679", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0060", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0060", "label": "PP1", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1678/1680", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "Answer from the lab who submitted the variant in Clinvar (PreventionGenetics) : Our patient had AML, a personal and family history of familial thrombocytopenia, easy bruising, and hypocellular marrow at diagnosis. The individual's mother also carried the variant and had thrombocytopenia. Although they were unavailable for testing, the maternal grandmother and great-grandfather also were reported to have easy bruising. The maternal great-grandfather died of leukemia in his 60s. ==> 2 meioses with positive genotype instead of 3.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1678/1680", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1679", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1678", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1837", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1838", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0061", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0061", "label": "PP2", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1837/1839", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This rule is not applicable to the MMVCEP.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1837/1839", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1838", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1837", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1747", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1748", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0062", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0062", "label": "PP3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1747/1749", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This missense variant has a REVEL score ≥ 0.88 (0.962) (PP3). SpliceAI score is null.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1747/1749", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1748", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1747", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1633", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1634", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/CA410207974/MONDO:0011071/008/el/0/1633/1635", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This rule is not applicable to the MMVCEP.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1633/1635", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1634", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1633", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1702", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1703", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0069", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000328", "id": "SEPIO:0000328", "label": "Benign Strong" }, "id": "0069", "label": "BS2", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1702/1704", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1702/1704", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1703", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1702", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1636", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1637", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/CA410207974/MONDO:0011071/008/el/0/1636/1638", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This variant is completely absent from all population databases with at least 20x coverage for RUNX1 in gnomAD v2.1.1 and v3.1.2 (PM2_supporting).", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1636/1638", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1637", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1636", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1606", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1607", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0032", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0032", "label": "PS4", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1606/1608", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": 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The individual's mother also carried the variant and had thrombocytopenia. Although they were unavailable for testing, the maternal grandmother and great-grandfather also were reported to have easy bruising. The maternal great-grandfather died of leukemia in his 60s.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1606/1608", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1607", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1606", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1684", "evidenceItem": [ { "@id": 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"CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1684", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1789", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1790", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0081", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000327", "id": "SEPIO:0000327", "label": "Benign Supporting" }, "id": "0081", "label": "BP3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1789/1791", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This rule is not applicable to the MMVCEP.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1789/1791", "type": 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"type": "Contribution" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0082", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000327", "id": "SEPIO:0000327", "label": "Benign Supporting" }, "id": "0082", "label": "BP1", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1726/1728", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This rule is not applicable to the MMVCEP.", "contributionDate": { "date": "2023/12/9", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": 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publication has reported this variant to date.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1597/1599", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1598", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1597", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1777", "evidenceItem": [ { "@id": 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], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0051", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000330", "id": "SEPIO:0000330", "label": "Pathogenic Strong" }, "id": "0051", "label": "PS2", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1663/1665", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "To our knowledge, no publication has reported this variant to date.", "contributionDate": { "date": "2023/12/9", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": 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"contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/006", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000216", "id": "SEPIO:0000216", "label": "Pathogenic Moderate" }, "id": "006", "label": "PM1", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1615/1617", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { 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Moderate" }, "id": "007", "label": "PM3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1717/1719", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This rule is not applicable to the MMVCEP.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": 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role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1804/1806", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1805", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1804", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1768", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1769", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0071", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000328", "id": "SEPIO:0000328", "label": "Benign Strong" }, "id": "0071", "label": "BS4", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1768/1770", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "Clinvar has one entry for this variant but the affected status is unknown. 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"@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1589", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0072", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000328", "id": "SEPIO:0000328", "label": "Benign Strong" }, "id": "0072", "label": "BS3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1588/1590", "evidenceItem": [ { "@id": 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"EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1580", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1579", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1654", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1655", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/0079", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000327", "id": "SEPIO:0000327", "label": "Benign Supporting" }, "id": "0079", "label": "BP7", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1654/1656", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This is a missense variant.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1654/1656", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1655", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1654", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1591", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/ei/1/1592", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "contributionDate": { "date": "2023/12/9", "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/009", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000216", "id": "SEPIO:0000216", "label": "Pathogenic Moderate" }, "id": "009", "label": "PM4", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA410207974/MONDO:0011071/008/el/0/1591/1593", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50034_EP156503333731505", "id": "CG-PCER-AGENT:CG_50034_EP156503333731505", "type": "Agent" }, "comments": "This variant is a missense.", "contributionDate": { "date": "2023/12/9", "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": "CA410207974/MONDO:0011071/008/ci/CA410207974/MONDO:0011071/008.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1591/1593", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/1/1592", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008/0/1591", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA410207974/MONDO:0011071/008", "metadata": { "created": "2024-09-28T03:28:46.572Z", "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": "Sat, 28 Sep 2024 03:28:46 -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": "9e51dbad-5cbe-4a99-8a12-f7daf29fd7ab", "variant": { "@id": "https://reg.genome.network/allele/CA410207974", "id": "CAR:CA410207974", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_001754.5:c.593A>C" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_001754.5(RUNX1):c.593A>C (p.Asp198Ala)" } ], "type": "CAR" } } ], "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-04-04T15:09:28.716Z" } }, "status": { "code": 200, "name": "OK" } }