ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.8298C>T (p.Ser2766=)

gnomAD frequency: 0.00102  dbSNP: rs145850037
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000247147 SCV000305792 likely benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001000432 SCV001157246 benign Polycystic kidney disease, adult type 2019-03-24 criteria provided, single submitter clinical testing
GeneDx RCV001564260 SCV001787398 likely benign not provided 2021-05-25 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 12007219, 16430766, 17574468)
CeGaT Center for Human Genetics Tuebingen RCV001564260 SCV004142839 benign not provided 2022-08-01 criteria provided, single submitter clinical testing PKD1: BS1, BS2
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354014 SCV000592821 benign Bile duct cancer no assertion criteria provided clinical testing The PKD1 p.Ser2766Ser variant was identified in 3 of 246 proband chromosomes (frequency: 0.012) from Japanese, Slovenian and American individuals or families with ADPKD, co-occurring with a pathogenic splicing PKD1 variant (c.8228-2delAG) in 1 Japanese individual (Garcia-Gonzalez 2007, Vouk 2006, Inoue 2002). The variant was also identified by our laboratory in an individual with ADPKD, co-occurring with a pathogenic PKD1 variant (c.2215C>T), increasing the likelihood that the p.Ser2766Ser variant does not have clinical significance. The variant was also identified in dbSNP (ID: rs145850037) as “NA”, and the ADPKD Mutation Database (classification likely neutral) and in the ClinVar database classified as Likely Benign by Prevention Genetics, but was not found in PKD1-LOVD, Clinvitae, GeneInsight COGR, MutDB and PKD1-LOVD 3.0. This variant was identified in the 1000 Genomes Project in 5 of 5000 chromosomes (frequency: 0.001), NHLBI GO Exome Sequencing Project in 21 of 8552 European American alleles (frequency: 0.0025) and in 5 of 4352 African American alleles (frequency: 0.0011), the Exome Aggregation Consortium database (August 8, 2016) in 118 of 115912 chromosomes (freq. 0.0010)) in the following populations: European (Non-Finnish) in 95 of 63278 chromosomes (freq. 0.0015), African in 11 of 8940 chromosomes (freq. 0.0012), Latino in 9 of 11392 chromosomes (freq. 0.00079), South Asian in 3 of 16460 chromosomes (freq. 00018), but was not seen in East Asian, Finnish, or Other populations; increasing the likelihood this could be a low frequency benign variant. The p.Ser2766Ser 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. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign.

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