ClinVar Miner

Submissions for variant NM_000297.4(PKD2):c.1830G>A (p.Ala610=)

gnomAD frequency: 0.00091  dbSNP: rs144968710
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Preventiongenetics, part of Exact Sciences RCV000243588 SCV000303530 benign not specified criteria provided, single submitter clinical testing
Invitae RCV000756538 SCV000658969 benign Autosomal dominant polycystic kidney disease 2024-01-14 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000999906 SCV000884373 likely benign Polycystic kidney disease 2 2019-12-27 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000999906 SCV001316014 likely benign Polycystic kidney disease 2 2017-04-28 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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
GeneDx RCV001561555 SCV001784181 likely benign not provided 2021-09-23 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 24658975)
Athena Diagnostics Inc RCV000243588 SCV001879469 benign not specified 2021-01-21 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001561555 SCV004152958 likely benign not provided 2022-11-01 criteria provided, single submitter clinical testing PKD2: BP4, BP7, BS1
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001291924 SCV000592880 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD2 p.Ala610Ala variant was identified in dbSNP (ID: rs144968710) as “N/A”, ADPKD Mutation Database (likely neutral), 1000 Genomes Project in 8 of 5000 chromosomes (frequency: 0.002), NHLBI GO Exome Sequencing Project in 8 of 8600 European American and in 10 of 4406 African American alleles, the Exome Aggregation Consortium database (August 8, 2016) in 94 of 121226 chromosomes (freq. 0.0008) in the following populations: European in 39 of 66662 chromosomes (freq. 0.0006), African in 19 of 10406 chromosomes (freq. 0.002), South Asian in 19 of 16482 chromosomes (freq. 0.001), Latino in 12 of 11560 chromosomes (freq. 0.001), Finish in 3 of 6600 chromosomes (freq. 0.0005), Other 2 in 906 chromosomes (freq. 0.002), increasing the likelihood this could be a low frequency benign variant. The p.Ala610Ala variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs outside of the splicing consensus sequence and 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. 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.
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000243588 SCV001978270 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001561555 SCV001980428 likely benign not provided no assertion criteria provided clinical testing

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