{ "data": [ { "@context": "https://erepo.genome.network/evrepo/api/context", "@id": "https://cgerepoapi/evrepo/api/summary/classification/16f373e0-f3cf-4ebe-91ea-6d1a22e44f9c/doc/sepio/version/1.0.0", "assertionMethod": { "type": "VariantPathogenicityInterpretationGuideline" }, "condition": { "@id": "https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:0019501", "id": "MONDO:0019501", "label": "Usher syndrome", "type": "GeneticCondition" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1684", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/ei/1/1685", "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/0080", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000327", "id": "SEPIO:0000327", "label": "Benign Supporting" }, "id": "0080", "label": "BP4", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1684/1686", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "Our cutoff is >0.7 and the variant is 0.786, so PP3 is met. No splicing impact is predicted.", "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": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1684/1686", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1685", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1684", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1789", "evidenceItem": [ { "@id": 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"CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1789", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1726", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/ei/1/1727", "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/0082", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000327", "id": "SEPIO:0000327", "label": "Benign Supporting" }, "id": "0082", "label": "BP1", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1726/1728", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "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" } ], "id": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1726/1728", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1727", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1726", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1597", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/ei/1/1598", "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/0084", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000327", "id": "SEPIO:0000327", "label": "Benign Supporting" }, "id": "0084", "label": "BP2", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1597/1599", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000427", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "67 Chinese families with Usher syndrome were tested for variants in 196 retinal disease genes. The p.Gly1861Ser variant was identified 1 patient with c.8559-2A>G in trans.", "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": "CA262105/MONDO:0019501/005/ci/EV000000427", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/26338283", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000426", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "This is a case report of a Chinese family with pseudo-dominant Usher syndrome. The proband is compound het for p.Gly1861Ser and p.C934W. There is also an affected brother who has this genotype.", "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": "CA262105/MONDO:0019501/005/ci/EV000000426", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/26310143", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000428", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "5 unrelated Chinese families with Usher syndrome were tested using a panel of 144 known genes for deep exome resequencing. The p.Gly1861Ser variant was identified in family F2 in trans with a novel frameshift c.8602delA, but was in cis with a second missense variant p.R5143C. The cis variants were also present in an unaffected sib.", "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": "CA262105/MONDO:0019501/005/ci/EV000000428", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/23737954", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000429", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "179 unrelated Chinese patients with inherited retinal dystrophy were tested for variants in 164 known genes. The p.Gly1861Ser variant was identified in 2 patients with Usher syndrome. The patients were compound het for p.G1526R and p.R5143C, respectively. I hesitate to count the patient with the p.R5143C variant in trans because this is the same author that identified that variant in cis in a patient.\n\nNOTE: p.R5143C is benign due to a MAF OF 0.9% in East Asians, and based on Huang 2013, variants likely in cis. Did not count proband with this variant (Andrea)", "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": "CA262105/MONDO:0019501/005/ci/EV000000429", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/25356976", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1597/1599", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1598", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1597", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1777", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/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": "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/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/CA262105/MONDO:0019501/005/el/0/1777/1779", "evidenceItem": [ { "@id": 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this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1828/1830", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1829", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1828", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1735", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/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": "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/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/CA262105/MONDO:0019501/005/el/0/1735/1737", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "Cases: 5/504 Asian alleles\ngnomAD: 3/17184 Asian alleles\n\nChi-square with Yates correction: Chi squared equals 82.448 with 1 degrees of freedom. The two-tailed P value is less than 0.0001.The association between rows (groups) and columns (outcomes) is considered to be extremely statistically significant.", "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": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1735/1737", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1736", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1735", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1651", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/ei/1/1652", "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/0058", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000330", "id": "SEPIO:0000330", "label": "Pathogenic Strong" }, "id": "0058", "label": "PM3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1651/1653", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000427", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "67 Chinese families with Usher syndrome were tested for variants in 196 retinal disease genes. The p.Gly1861Ser variant was identified 1 patient with c.8559-2A>G in trans.", "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": "CA262105/MONDO:0019501/005/ci/EV000000427", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/26338283", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000426", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "This is a case report of a Chinese family with pseudo-dominant Usher syndrome. The proband is compound het for p.Gly1861Ser and p.C934W. There is also an affected brother who has this genotype.", "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": "CA262105/MONDO:0019501/005/ci/EV000000426", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/26310143", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000428", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "5 unrelated Chinese families with Usher syndrome were tested using a panel of 144 known genes for deep exome resequencing. The p.Gly1861Ser variant was identified in family F2 in trans with a novel frameshift c.8602delA, but was in cis with a second missense variant p.R5143C. The cis variants were also present in an unaffected sib.", "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": "CA262105/MONDO:0019501/005/ci/EV000000428", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/23737954", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000429", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "179 unrelated Chinese patients with inherited retinal dystrophy were tested for variants in 164 known genes. The p.Gly1861Ser variant was identified in 2 patients with Usher syndrome. The patients were compound het for p.G1526R and p.R5143C, respectively. I hesitate to count the patient with the p.R5143C variant in trans because this is the same author that identified that variant in cis in a patient.\n\nNOTE: p.R5143C is benign due to a MAF OF 0.9% in East Asians, and based on Huang 2013, variants likely in cis. Did not count proband with this variant (Andrea)", "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": "CA262105/MONDO:0019501/005/ci/EV000000429", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/25356976", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1651/1653", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1652", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1651", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1804", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/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/CA262105/MONDO:0019501/005/el/0/1804/1806", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "Variant is too frequent to meet PM2_supporting.\n\n-ANDREA: disagree; meets PM2 supporting, since it is at 0.017% of East Asian chroms and cutoff is 0.07%.", "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": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1804/1806", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1805", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1804", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1768", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/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/CA262105/MONDO:0019501/005/el/0/1768/1770", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/EV000000426", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50007_EP155190799758139", "id": "CG-PCER-AGENT:CG_50007_EP155190799758139", "type": "Agent" }, "comments": "This is a case report of a Chinese family with pseudo-dominant Usher syndrome. The proband is compound het for p.Gly1861Ser and p.C934W. There is also an affected brother who has this genotype.", "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": "CA262105/MONDO:0019501/005/ci/EV000000426", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/26310143", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1768/1770", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1769", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1768", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1588", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/ei/1/1589", "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/0072", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000328", "id": "SEPIO:0000328", "label": "Benign Strong" }, "id": "0072", "label": "BS3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1588/1590", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "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" } ], "id": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1588/1590", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1589", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1588", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1579", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/ei/1/1580", "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/0078", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000327", "id": "SEPIO:0000327", "label": "Benign Supporting" }, "id": "0078", "label": "BP5", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1579/1581", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "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" } ], "id": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1579/1581", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1580", "statementOutcome": { 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"https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1780/1782", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "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" } ], "id": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1780/1782", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1781", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1780", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1591", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/ei/1/1592", "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/009", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000216", "id": "SEPIO:0000216", "label": "Pathogenic Moderate" }, "id": "009", "label": "PM4", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA262105/MONDO:0019501/005/el/0/1591/1593", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "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" } ], "id": "CA262105/MONDO:0019501/005/ci/CA262105/MONDO:0019501/005.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1591/1593", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/1/1592", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005/0/1591", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA262105/MONDO:0019501/005", "metadata": { "created": "2024-09-27T19:41:26.256Z", "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 19:41:26 -0000", "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)", "version": "1.0.0" }, "statementOutcome": { "@id": "https://loinc.org/LA6668-3", "id": "LN:LA6668-3", "label": "Pathogenic" }, "type": "VariantPathogenicityInterpretation", "uuid": "16f373e0-f3cf-4ebe-91ea-6d1a22e44f9c", "variant": { "@id": "https://reg.genome.network/allele/CA262105", "id": "CAR:CA262105", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_206933.2:c.5581G>A" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_206933.2(USH2A):c.5581G>A (p.Gly1861Ser)" } ], "type": "CAR" } } ], "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-11-04T00:56:19.333Z" } }, "status": { "code": 200, "name": "OK" } }