ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.11682C>T (p.Ser3894=)

gnomAD frequency: 0.01235  dbSNP: rs567482892
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Preventiongenetics, part of Exact Sciences RCV000247104 SCV000305683 benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000576449 SCV000604708 benign Polycystic kidney disease, adult type 2018-09-25 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000576449 SCV000677390 benign Polycystic kidney disease, adult type 2017-05-30 criteria provided, single submitter clinical testing
GeneDx RCV001706303 SCV001858328 benign not provided 2020-10-22 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 15772804, 17574468, 18837007, 22008521, 22383692, 24374109)
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001291848 SCV000592855 benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Ser3894Ser variant was identified in 11 of 1112 proband chromosomes (frequency: 0.01) from individuals or families with ADPKD (Bataille 2011, Garcia-Gonzalez 2007, Rossetti 2012, Peltola 2005). The variant was also identified in dbSNP (ID: rs567482892) as “N/A” and the ADPKD Mutation Database (as likely neutral). This variant was identified in the 1000 Genomes Project in 21 of 5000 chromosomes (frequency: 0.004), the Exome Aggregation Consortium database (August 8, 2016) in 8 (1 homozygous) of 462 chromosomes (freq. 0.02) in the following populations: European in 5 of 40 chromosomes (freq. 0.13), Finnish in 1 of 2 chromosomes (freq. 0.5), Latino in 1 of 10 chromosomes (freq. 0.1), South Asian in 1 of 398 chromosomes (freq. 0.003), although this low number of observations and low frequency is not substantive enough to determine the prevalence of the variant in the general population and its relationship to disease. The p.Ser3894Ser 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 addition, the variant classified as a polymorphism by number of population and research studies (Bataille 2011, Garcia-Gonzalez 2007, Rossetti 2012, Peltola 2005). In summary, based on the above information, this variant meets our laboratory criteria to be classified as benign.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000247104 SCV001799346 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000247104 SCV001951158 benign not specified no assertion criteria provided clinical testing

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