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The variant was seen in one affected patient without a second variant.", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000422", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/16570074", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000424", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "57 EVA patients screened for SLC26A4. Found in one patinet with HL and EVA but a normal perchlorate test. Did not note a second variant. Variant was absent from 100 control chromosomes-no family/race info", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000424", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/10700480", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000104", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "1119 patients with hearing loss tested. 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The variant was seen in one affected patient without a second variant.", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000422", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/16570074", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000424", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "57 EVA patients screened for SLC26A4. Found in one patinet with HL and EVA but a normal perchlorate test. Did not note a second variant. Variant was absent from 100 control chromosomes-no family/race info", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000424", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/10700480", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000104", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "1119 patients with hearing loss tested. Found one compound heterozygote with this variant in trans with a splicing c.-4+1G>C variant with severe to profound hearing loss, but not noted if they tested temporal bone imaging. Shouldn't be used for PM3, as the splice variant is VUS.", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000104", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/26969326", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1597/1599", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/1/1598", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1597", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1645", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/ei/1/1646", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "contributionDate": { "date": "2023/1/25", "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/CA132727/MONDO:0010134/005/el/0/1645/1647", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000425", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "Noted variant lacking experimentally validated functional information. Conserved and gives NeEMO stability 1.37. Predicted Benign in silico. predicted molecular effect maintenance of hydrophobicity.", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000425", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/27771369", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000423", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "This study investigated the impact of 9 different SLC26A4 variants on protein function. They found that the L117F variant showed a cell membrane protein distribution similar to that of the wild type protein and exhibited a rate of iodide efflux statistically similar to that of the WT. this study actually questioned as to whether there was an alternate cause in the case from the study. This study would support a benign impact of the variant, however it is also important to note that this study didn't investigate all ion transport functions.", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000423", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/11932316", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1645/1647", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/1/1646", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1645", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1777", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/ei/1/1778", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "contributionDate": { "date": "2023/1/25", "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/0087", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000325", "id": "SEPIO:0000325", "label": "Benign Stand Alone" }, "id": "0087", "label": "BA1", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1777/1779", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/CA132727/MONDO:0010134/005.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "The filtering allele frequency of the p.Leu117Phe variant is 0.005208 (54/10368 alleles) for Ashkenazi Jewish chromosomes in gnomAD v2.1.1, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). The ClinGen Hearing Loss Expert Panel believes that the evidence for the pathogenicity of this variant for hearing loss outweighs the high allele frequency of the variant in population databases. 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"CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1828/1830", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/1/1829", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1828", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1735", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/ei/1/1736", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "contributionDate": { "date": "2023/1/25", "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/0053", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000330", "id": "SEPIO:0000330", "label": "Pathogenic Strong" }, "id": "0053", "label": "PS4", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1735/1737", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000422", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "109 patients from 100 families with nonsyndromic hearing loss and EVA. 50 control individuals, study in France. The variant was seen in one affected patient without a second variant.", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000422", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/16570074", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000424", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "57 EVA patients screened for SLC26A4. Found in one patinet with HL and EVA but a normal perchlorate test. Did not note a second variant. Variant was absent from 100 control chromosomes-no family/race info.", "contributionDate": { "date": "2023/1/25", "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": "CA132727/MONDO:0010134/005/ci/EV000000424", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/10700480", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000104", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "1119 patients with hearing loss tested. 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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 01:12:40 -0000", "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)", "version": "2.0.0" }, "statementOutcome": { "@id": "https://loinc.org/LA6668-3", "id": "LN:LA6668-3", "label": "Pathogenic" }, "type": "VariantPathogenicityInterpretation", "uuid": "67c2f97e-385f-494a-b06e-701135ace536", "variant": { "@id": "https://reg.genome.network/allele/CA132727", "id": "CAR:CA132727", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000441.1:c.349C>T" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000441.1(SLC26A4):c.349C>T" } ], "type": "CAR" } }, { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/67c2f97e-385f-494a-b06e-701135ace536/doc/sepio/version/1.0.0", "assertionMethod": { "type": "VariantPathogenicityInterpretationGuideline" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0010134", "id": "MONDO:0010134", "label": "Pendred syndrome", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1804", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/ei/1/1805", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "contributionDate": { "date": "2019/7/17", "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/0070", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000328", "id": "SEPIO:0000328", "label": "Benign Strong" }, "id": "0070", "label": "BS1", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1804/1806", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/CA132727/MONDO:0010134/005.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "Despite having a filtered allele frequency in Ashkenazi Jewish population in gnomAD of 0.4%, this variant is on the ClinGen Hearing Loss Expert Panel's exclusion list for BS1.", "contributionDate": { "date": "2019/7/17", "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": "CA132727/MONDO:0010134/005/ci/CA132727/MONDO:0010134/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1804/1806", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/1/1805", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1804", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1768", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/ei/1/1769", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "contributionDate": { "date": "2019/7/17", "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/CA132727/MONDO:0010134/005/el/0/1768/1770", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/CA132727/MONDO:0010134/005.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "There are 2 family members in LMM's internal data who are unaffected but are heterozygous for the p.Leu117Phe variant. 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Found one compound heterozygote with this variant in trans with a splicing c.-4+1G>C variant with severe to profound hearing loss, but not noted if they tested temporal bone imaging. Shouldn't be used for PM3, as the splice variant is VUS.", "contributionDate": { "date": "2019/7/17", "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": "CA132727/MONDO:0010134/005/ci/EV000000104", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/26969326", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1597/1599", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/1/1598", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1597", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1645", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/ei/1/1646", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "contributionDate": { "date": "2019/7/17", "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/CA132727/MONDO:0010134/005/el/0/1645/1647", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000423", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "This study investigated the impact of 9 different SLC26A4 variants on protein function. They found that the L117F variant showed a cell membrane protein distribution similar to that of the wild type protein and exhibited a rate of iodide efflux statistically similar to that of the WT. this study actually questioned as to whether there was an alternate cause in the case from the study. 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}, "id": "0053", "label": "PS4", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1735/1737", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000422", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "109 patients from 100 families with nonsyndromic hearing loss and EVA. 50 control individuals, study in France. 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Variant was absent from 100 control chromosomes-no family/race info.", "contributionDate": { "date": "2019/7/17", "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": "CA132727/MONDO:0010134/005/ci/EV000000424", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/10700480", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/EV000000104", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "1119 patients with hearing loss tested. Found one compound heterozygote with this variant in trans with a splicing c.-4+1G>C variant with severe to profound hearing loss, but not noted if they tested temporal bone imaging. Shouldn't be used for PM3, as the splice variant is VUS.", "contributionDate": { "date": "2019/7/17", "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": "CA132727/MONDO:0010134/005/ci/EV000000104", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/26969326", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1735/1737", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/1/1736", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1735", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1648", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/ei/1/1649", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "contributionDate": { "date": "2019/7/17", "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/0023", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000330", "id": "SEPIO:0000330", "label": "Pathogenic Strong" }, "id": "0023", "label": "PP1", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA132727/MONDO:0010134/005/el/0/1648/1650", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA132727/MONDO:0010134/005/ci/CA132727/MONDO:0010134/005.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "This variant segregates with disease in at least 3 affected and 4 unaffected individuals from Karen Avraham's lab. They also report an additional 5 Ashkenzazi families with segregation of this variant and HL.\n\nRS10/9/18 Update: Variant seen in 7 affected homozygous individuals and 3 affected heterozygous individuals, only one of whom has a second variant identified in trans. At least 4 homozygous segregations meets criteria for strong.", "contributionDate": { "date": "2019/7/17", "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": "CA132727/MONDO:0010134/005/ci/CA132727/MONDO:0010134/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1648/1650", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/1/1649", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005/0/1648", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA132727/MONDO:0010134/005", "metadata": { "created": "2024-09-27T19:41:11.568Z", "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, 27 Sep 2024 19:41:11 -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": "67c2f97e-385f-494a-b06e-701135ace536", "variant": { "@id": "https://reg.genome.network/allele/CA132727", "id": "CAR:CA132727", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000441.1:c.349C>T" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000441.1(SLC26A4):c.349C>T" } ], "type": "CAR" } } ], "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-11-04T11:41:47.369Z" } }, "status": { "code": 200, "name": "OK" } }