ClinVar Miner

Submissions for variant NM_000297.4(PKD2):c.595+15C>T

gnomAD frequency: 0.00026  dbSNP: rs559555727
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 5
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000507327 SCV000604836 benign not specified 2017-03-25 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001155351 SCV001316775 uncertain significance Polycystic kidney disease 2 2017-04-27 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). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
GeneDx RCV001561763 SCV001784420 likely benign not provided 2020-01-27 criteria provided, single submitter clinical testing
Invitae RCV002056911 SCV002408229 benign Autosomal dominant polycystic kidney disease 2023-12-19 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292346 SCV001480701 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD2 c.595+15C>T variant was not identified in the literature nor was it identified in the LOVD 3.0, ADPKD Mutation Database and PKD2-LOVD databases. It was identified in dbSNP (ID: rs559555727) as "With Benign Allele" and ClinVar (classified as 1x Benign by ARUP Laboratories). The variant was also identified in control databases in 156 of 138366 chromosomes (1 homozygous) at a frequency of 0.001 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 1 of 3982 chromosomes (freq: 0.0003), Latino in 1 of 21870 chromosomes (freq: 0.00005), European in 2 of 54006 chromosomes (freq: 0.00004), East Asian in 150 of 9980 chromosomes (freq: 0.02), and South Asian in 2 of 20178 chromosomes (freq: 0.0001), while the variant was not observed in the African, Ashkenazi Jewish and Finnish populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely 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.