{ "data": { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/f6ace292-1671-4377-b486-c8abc2aaf55b/doc/sepio/version/1.0.0", "assertionMethod": { "@id": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/1570648177", "label": "ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RS1 Version 1.0.0", "type": "VariantPathogenicityInterpretationGuideline", "version": "1.0.0" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0010725", "id": "MONDO:0010725", "label": "X-linked retinoschisis", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA515477887/MONDO:0010725/126/el/0/1798", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA515477887/MONDO:0010725/126/ei/1/1799", "contribution": [ { 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"https://erepo.genome.network/evrepo/api/interpretation/CA515477887/MONDO:0010725/126/el/0/1684", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA515477887/MONDO:0010725/126/ei/1/1685", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50086_EP174775864491222", "id": "CG-PCER-AGENT:CG_50086_EP174775864491222", "type": "Agent" }, "contributionDate": { "date": "2025/9/23", "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/CA515477887/MONDO:0010725/126/el/0/1684/1686", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA515477887/MONDO:0010725/126/ci/CA515477887/MONDO:0010725/126.002", "contribution": [ { "agent": { "@id": 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"CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA515477887/MONDO:0010725/126/0/1684", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA515477887/MONDO:0010725/126/el/0/1804", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA515477887/MONDO:0010725/126/ei/1/1805", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50086_EP174775864491222", "id": "CG-PCER-AGENT:CG_50086_EP174775864491222", "type": "Agent" }, "contributionDate": { "date": "2025/9/23", "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/CA515477887/MONDO:0010725/126/el/0/1804/1806", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA515477887/MONDO:0010725/126/ci/CA515477887/MONDO:0010725/126.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50086_EP174775864491222", "id": "CG-PCER-AGENT:CG_50086_EP174775864491222", "type": "Agent" }, "comments": "This variant is present in gnomAD v4.1.0 at a frequency of 0.000007745 among hemizygous individuals, with 3 variant alleles / 387,371 total alleles, which is between the ClinGen X-linked IRD VCEP PM2_Supporting threshold of <0.000002 and BS1 threshold of >0.00002 and fails to meet these criteria.", "contributionDate": { "date": "2025/9/23", "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": "CA515477887/MONDO:0010725/126/ci/CA515477887/MONDO:0010725/126.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA515477887/MONDO:0010725/126/0/1804/1806", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA515477887/MONDO:0010725/126/1/1805", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA515477887/MONDO:0010725/126/0/1804", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA515477887/MONDO:0010725/126/el/0/1654", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA515477887/MONDO:0010725/126/ei/1/1655", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50086_EP174775864491222", "id": "CG-PCER-AGENT:CG_50086_EP174775864491222", "type": "Agent" }, "contributionDate": { "date": "2025/9/23", "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/CA515477887/MONDO:0010725/126/el/0/1654/1656", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA515477887/MONDO:0010725/126/ci/CA515477887/MONDO:0010725/126.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50086_EP174775864491222", "id": "CG-PCER-AGENT:CG_50086_EP174775864491222", "type": "Agent" }, "comments": "This silent variant c.177T>C causing a synonymous variant at codon 59 does not have an impact at splicing sites according to Splice AI, which predicts a delta score of 0.00 for all predictive splice changes, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP7).", "contributionDate": { "date": "2025/9/23", "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": "CA515477887/MONDO:0010725/126/ci/CA515477887/MONDO:0010725/126.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA515477887/MONDO:0010725/126/0/1654/1656", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA515477887/MONDO:0010725/126/1/1655", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA515477887/MONDO:0010725/126/0/1654", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA515477887/MONDO:0010725/126", "metadata": { "created": "2025-09-23T20:23:32.276Z", "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": "Tue, 23 Sep 2025 20:23:32 -0000", "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)", "version": "1.0.0" }, "statementOutcome": { "@id": "https://loinc.org/LA26334-5", "id": "LN:LA26334-5", "label": "Likely Benign" }, "type": "VariantPathogenicityInterpretation", "uuid": "f6ace292-1671-4377-b486-c8abc2aaf55b", "variant": { "@id": "https://reg.genome.network/allele/CA515477887", "id": "CAR:CA515477887", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000330.4:c.177T>C" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000330.4(RS1):c.177T>C (p.Cys59=)" } ], "type": "CAR" } }, "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-11-12T10:09:29.703Z" } }, "status": { "code": 200, "name": "OK" } }