ClinVar Miner

Submissions for variant NM_020433.5(JPH2):c.483G>A (p.Thr161=)

gnomAD frequency: 0.00023  dbSNP: rs746384802
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 6
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000244330 SCV000320074 likely benign Cardiovascular phenotype 2015-09-10 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GeneDx RCV000841265 SCV000983224 likely benign not provided 2020-11-10 criteria provided, single submitter clinical testing
Invitae RCV001087143 SCV001005172 benign Hypertrophic cardiomyopathy 2023-10-11 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000841265 SCV002064043 likely benign not provided 2021-10-01 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003909888 SCV004726865 likely benign JPH2-related disorder 2020-11-15 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003993909 SCV004813179 benign not specified 2024-02-12 criteria provided, single submitter clinical testing Variant summary: JPH2 c.483G>A alters a non-conserved nucleotide resulting in a synonymous change. Consensus agreement among computation 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 0.00022 in 152954 control chromosomes, predominantly at a frequency of 0.00078 within the South Asian subpopulation in the gnomAD database. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 30 fold of the estimated maximal expected allele frequency for a pathogenic variant in JPH2 causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. To our knowledge, no occurrence of c.483G>A in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 264268). Based on the evidence outlined above, the variant was classified as benign.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.