{ "data": { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/7af2f998-2e92-4fe3-a10d-a16cc797dd3e/doc/sepio/version/1.0.0", "assertionMethod": { "@id": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/135637575", "label": "ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.0.0", "type": "VariantPathogenicityInterpretationGuideline", "version": "3.0.0" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0017623", "id": "MONDO:0017623", "label": "PTEN hamartoma tumor syndrome", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA377784410/MONDO:0017623/003/el/0/1645", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA377784410/MONDO:0017623/003/ei/1/1646", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2023/10/19", "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/0085", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000327", "id": "SEPIO:0000327", "label": "Benign Supporting" }, "id": "0085", "label": "BS3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA377784410/MONDO:0017623/003/el/0/1645/1647", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA377784410/MONDO:0017623/003/ci/CA377784410/MONDO:0017623/003.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Mighell PMID: 29706350 (0.225696942) WT_like, BS3_supp\n", "contributionDate": { "date": "2023/10/19", "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": "CA377784410/MONDO:0017623/003/ci/CA377784410/MONDO:0017623/003.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/0/1645/1647", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/1/1646", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/0/1645", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA377784410/MONDO:0017623/003/el/0/1663", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA377784410/MONDO:0017623/003/ei/1/1664", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2023/10/19", "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/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/CA377784410/MONDO:0017623/003/el/0/1663/1665", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA377784410/MONDO:0017623/003/ci/CA377784410/MONDO:0017623/003.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. 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"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/CA377784410/MONDO:0017623/003/el/0/1747/1749", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA377784410/MONDO:0017623/003/ci/CA377784410/MONDO:0017623/003.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "REVEL score: 0.919 (>0.7)", "contributionDate": { "date": "2023/10/19", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": 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"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/CA377784410/MONDO:0017623/003/el/0/1636/1638", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA377784410/MONDO:0017623/003/ci/CA377784410/MONDO:0017623/003.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Absent in large sequenced populations OR present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (PMID 27535533).", "contributionDate": { "date": "2023/10/19", "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": "CA377784410/MONDO:0017623/003/ci/CA377784410/MONDO:0017623/003.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/0/1636/1638", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/1/1637", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/0/1636", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA377784410/MONDO:0017623/003/el/0/1606", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA377784410/MONDO:0017623/003/ei/1/1607", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2023/10/19", "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/CA377784410/MONDO:0017623/003/el/0/1606/1608", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA377784410/MONDO:0017623/003/ci/CA377784410/MONDO:0017623/003.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "GeneDx case: de novo via exome trio in child with extreme macrocephaly, hydrocephalus, GI polyps, motor delay, brain venous anomaly. Gets PS2 and 1 point towards PS4_P\n", "contributionDate": { "date": "2023/10/19", "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": "CA377784410/MONDO:0017623/003/ci/CA377784410/MONDO:0017623/003.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/0/1606/1608", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/1/1607", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003/0/1606", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA377784410/MONDO:0017623/003", "metadata": { "created": "2024-09-28T03:09:52.037Z", "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 03:09:51 -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": "7af2f998-2e92-4fe3-a10d-a16cc797dd3e", "variant": { "@id": "https://reg.genome.network/allele/CA377784410", "id": "CAR:CA377784410", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000314.8:c.91A>G" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000314.8(PTEN):c.91A>G (p.Asn31Asp)" } ], "type": "CAR" } }, "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-11-01T18:24:04.223Z" } }, "status": { "code": 200, "name": "OK" } }