{ "data": { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://erepo.genome.network/evrepo/api/summary/classification/5d5806fe-d0fd-42ef-8a0a-6c04d6bb025c/doc/sepio/version/1.0.0", "assertionMethod": { "@id": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/1535304680", "label": "ClinGen Cardiomyopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MYBPC3 Version 1.0.0", "type": "VariantPathogenicityInterpretationGuideline", "version": "1.0.0" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0005045", "id": "MONDO:0005045", "label": "hypertrophic cardiomyopathy", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1747", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/ei/1/1748", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "contributionDate": { "date": "2025/11/14", "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" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1747/1749", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "comments": "Computational prediction tools and conservation analyses suggest that this variant may impact the protein (PP3; REVEL score ≥0.70)", "contributionDate": { "date": "2025/11/14", "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": "CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1747/1749", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/1/1748", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1747", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1636", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/ei/1/1637", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "contributionDate": { "date": "2025/11/14", "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" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1636/1638", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "comments": "Absent in 2.1. gnomad", "contributionDate": { "date": "2025/11/14", "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": "CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1636/1638", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/1/1637", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1636", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1615", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/ei/1/1616", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "contributionDate": { "date": "2025/11/14", "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" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1615/1617", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "comments": "This variant lies in a region of the protein where variants are statistically more likely to be disease-associated (PM1_Strength; Walsh 2019 PMID: 30696458). ", "contributionDate": { "date": "2025/11/14", "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": "CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1615/1617", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/1/1616", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1615", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1684", "evidenceItem": [ { "@id": 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"https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/ei/1/1829", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "contributionDate": { "date": "2025/11/14", "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" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1828/1830", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "comments": "no functional studies", "contributionDate": { "date": "2025/11/14", "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": "CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1828/1830", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/1/1829", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1828", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1699", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/ei/1/1700", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "contributionDate": { "date": "2025/11/14", "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" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1699/1701", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "comments": "HCMR: 3/2633\nWalsh: 4/ 6179 HCM (2/2912 LMM, 2/3267 OMGL) --> LMM has now 5 cases/3200 and OMGL has at least 4 (see OMGL tab in variant excel spreadsheet) --->\nAssume 10,000 tested probands between OMGL, LMM , and other labs: 9 in 10000 case genotypes vs 1 in 56495 control genotypes gives an odds ratio of 50.89 (95%CI=6.45-401.72)\n\nLower bound CI:\nStrong 95%CI=6.45 (threshold for strong ≥20)\nModerate 95%CI=6.45 (threshold for moderate ≥10)\nSupporting 95%CI=6.45 (threshold for supporting ≥5)\n\nThe lower bound 95%CI is greater than 5 (95%CI=6.45). Therefore PS4 is set to PS4_Supporting\n\n\nLMM data with gnomad 2.1: 5 in 3200 case genotypes vs 1 in 56495 control genotypes gives an odds ratio of 88.41 (95%CI=10.33-756.96)\n\nLower bound CI:\nStrong 95%CI=10.33 (threshold for strong ≥20)\nModerate 95%CI=10.33 (threshold for moderate ≥10)\nSupporting 95%CI=10.33 (threshold for supporting ≥5)\n\nThe lower bound 95%CI is greater than 10 (95%CI=10.33). Therefore PS4 is set to PS4_Moderate\n\n Plus literature and ClinVar data, this would be at least Mod. \n\nDecipher only oxford data **** Please note that with gnomad 4.1, 12/1179878 alleles PS4_moderate is met. Feel more confident about this. (ran OR with walsh data)\n4 in 6179 case genotypes vs 12 in 589939 control genotypes gives an odds ratio of 31.84 (95%CI=10.27-98.76)\n\nLower bound CI:\nStrong 95%CI=10.27 (threshold for strong ≥20)\nModerate 95%CI=10.27 (threshold for moderate ≥10)\nSupporting 95%CI=10.27 (threshold for supporting ≥5)\n\nThe lower bound 95%CI is greater than 10 (95%CI=10.27). Therefore PS4 is set to PS4_Moderate", "contributionDate": { "date": "2025/11/14", "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": "CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1699/1701", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/1/1700", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1699", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1588", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/ei/1/1589", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "contributionDate": { "date": "2025/11/14", "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" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA010455/MONDO:0005045/095/el/0/1588/1590", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50002_EP155190197442076", "id": "CG-PCER-AGENT:CG_50002_EP155190197442076", "type": "Agent" }, "comments": "no functional studies", "contributionDate": { "date": "2025/11/14", "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": "CA010455/MONDO:0005045/095/ci/CA010455/MONDO:0005045/095.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1588/1590", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/1/1589", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095/0/1588", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA010455/MONDO:0005045/095", "metadata": { "created": "2025-11-14T06:55:03.670Z", "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, 14 Nov 2025 06:55:03 -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": "5d5806fe-d0fd-42ef-8a0a-6c04d6bb025c", "variant": { "@id": "https://reg.genome.network/allele/CA010455", "id": "CAR:CA010455", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000256.3:c.1483C>T" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000256.3(MYBPC3):c.1483C>T (p.Arg495Trp)" } ], "type": "CAR" } }, "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-07-27T13:39:10.283Z" } }, "status": { "code": 200, "name": "OK" } }