ClinVar Miner

Submissions for variant NM_002230.4(JUP):c.1159-13C>A

gnomAD frequency: 0.00258  dbSNP: rs201627219
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000039059 SCV000062737 likely benign not specified 2012-03-19 criteria provided, single submitter clinical testing 1159-13C>A in intron 7 of JUP: This variant is not expected to have clinical sig nificance because it has been identified in 0.8% (30/3738) African American chro mosomes from a broad population by the NHLBI Exome Sequencing Project (http://ev s.gs.washington.edu/EVS/). 1159-13C>A in intron 7 of JUP (allele frequency = 0. 8%, 30/3738) **
GeneDx RCV000039059 SCV000168909 benign not specified 2014-04-14 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Illumina Laboratory Services, Illumina RCV001125741 SCV001284843 likely benign Naxos disease 2017-10-09 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Laboratory Services, Illumina RCV001125742 SCV001284844 benign Arrhythmogenic right ventricular dysplasia 12 2017-10-09 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000039059 SCV001448538 benign not specified 2020-11-17 criteria provided, single submitter clinical testing Variant summary: JUP c.1159-13C>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0007 in 249090 control chromosomes, predominantly at a frequency of 0.0095 within the African or African-American subpopulation in the gnomAD database, including 2 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 1520 fold of the estimated maximal expected allele frequency for a pathogenic variant in JUP causing Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy phenotype (6.3e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.1159-13C>A in individuals affected with Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submitters (evaluation after 2014) cite the variant as likely benign/benign. Based on the evidence outlined above, the variant was classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001811276 SCV001473026 benign not provided 2019-12-27 criteria provided, single submitter clinical testing
Invitae RCV002054747 SCV002362243 benign Naxos disease; Arrhythmogenic right ventricular dysplasia 12 2024-01-31 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000039059 SCV001742122 benign not specified no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000039059 SCV001919887 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000039059 SCV001973989 benign not specified no assertion criteria provided clinical testing

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