{ "data": { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/71820217-a66e-4118-8cee-bda7afc0e944/doc/sepio/version/1.0.0", "assertionMethod": { "@id": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/1537428517", "label": "ClinGen Peroxisomal Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ABCD1 Version 1.0.0", "type": "VariantPathogenicityInterpretationGuideline", "version": "1.0.0" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0018544", "id": "MONDO:0018544", "label": "adrenoleukodystrophy", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA10549996/MONDO:0018544/105/el/0/1798", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA10549996/MONDO:0018544/105/ei/1/1799", "contribution": [ { "agent": { "@id": 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"https://erepo.genome.network/evrepo/api//agent/CG_50049_EP177618055787822", "id": "CG-PCER-AGENT:CG_50049_EP177618055787822", "type": "Agent" }, "contributionDate": { "date": "2026/4/15", "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/CA10549996/MONDO:0018544/105/el/0/1684/1686", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA10549996/MONDO:0018544/105/ci/CA10549996/MONDO:0018544/105.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50049_EP177618055787822", "id": "CG-PCER-AGENT:CG_50049_EP177618055787822", "type": "Agent" }, "comments": "The computational predictor REVEL gives a score of 0.357 which is below the threshold of 0.5, and the splice predictor SpliceAI indicated that the variant has no impact on splicing (score=0), evidence that does not predict a damaging effects on ABCD1 (BP4).", "contributionDate": { "date": "2026/4/15", "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": "CA10549996/MONDO:0018544/105/ci/CA10549996/MONDO:0018544/105.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/0/1684/1686", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/1/1685", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/0/1684", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA10549996/MONDO:0018544/105/el/0/1777", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA10549996/MONDO:0018544/105/ei/1/1778", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50049_EP177618055787822", "id": "CG-PCER-AGENT:CG_50049_EP177618055787822", "type": "Agent" }, "contributionDate": { "date": "2026/4/15", "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/CA10549996/MONDO:0018544/105/el/0/1777/1779", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA10549996/MONDO:0018544/105/ci/CA10549996/MONDO:0018544/105.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50049_EP177618055787822", "id": "CG-PCER-AGENT:CG_50049_EP177618055787822", "type": "Agent" }, "comments": "The filtering allele frequency of the c.692G>A variant in ABCD1 is 0.00001835 in gnomAD v2.1.1, 0.0001243 in gnomAD v3.1.2, and 0.0001243 (genomes) for all populations which is lower than the ClinGen Peroxisomal Disorders VCEP threshold (0.00017) for BA1, and therefore does not meet this criterion. ", "contributionDate": { "date": "2026/4/15", "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": "CA10549996/MONDO:0018544/105/ci/CA10549996/MONDO:0018544/105.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/0/1777/1779", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/1/1778", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/0/1777", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA10549996/MONDO:0018544/105/el/0/1804", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA10549996/MONDO:0018544/105/ei/1/1805", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50049_EP177618055787822", "id": "CG-PCER-AGENT:CG_50049_EP177618055787822", "type": "Agent" }, "contributionDate": { "date": "2026/4/15", "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/CA10549996/MONDO:0018544/105/el/0/1804/1806", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA10549996/MONDO:0018544/105/ci/CA10549996/MONDO:0018544/105.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50049_EP177618055787822", "id": "CG-PCER-AGENT:CG_50049_EP177618055787822", "type": "Agent" }, "comments": "The GrpMax filtering allele frequency of the c.692G>A variant in ABCD1 is 0.00009439 in the South Asian population in gnomAD v4.1, which is higher than the ClinGen Peroxisomal Disorders VCEP threshold of ≥0.000017 for BS1, and therefore meets this criterion (BS1). 9 hemizygotes are listed in total.", "contributionDate": { "date": "2026/4/15", "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": "CA10549996/MONDO:0018544/105/ci/CA10549996/MONDO:0018544/105.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/0/1804/1806", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/1/1805", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105/0/1804", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA10549996/MONDO:0018544/105", "metadata": { "created": "2026-04-15T15:07:32.312Z", "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, 15 Apr 2026 15:07:32 -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": "71820217-a66e-4118-8cee-bda7afc0e944", "variant": { "@id": "https://reg.genome.network/allele/CA10549996", "id": "CAR:CA10549996", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000033.4:c.692G>A" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000033.4(ABCD1):c.692G>A (p.Arg231Gln)" } ], "type": "CAR" } }, "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-10-14T17:17:23.228Z" } }, "status": { "code": 200, "name": "OK" } }