ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.588C>T (p.Ser196=) (rs776302294)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000245506 SCV000305760 likely benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000245506 SCV000604712 likely benign not specified 2016-10-20 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000245506 SCV000614511 benign not specified 2017-03-13 criteria provided, single submitter clinical testing
GeneDx RCV001568560 SCV001792453 likely benign not provided 2020-12-14 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 17574468)
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001292432 SCV001480902 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Ser196= variant was identified in 2 of 164 proband chromosomes (frequency: 0.01) from individuals or families with ADPKD (Garcia-Gonzalez 2007). The variant was also identified in dbSNP (ID: rs776302294) as "With other allele ", ClinVar (classified as benign by Athena Diagnostics; as likely benign by PreventionGenetics and ARUP), and in ADPKD Mutation Database (likely neutral). The variant was not identified in LOVD 3.0, or PKD1-LOVD, databases. The variant was identified in control databases in 342 of 159848 chromosomes (3 homozygous) at a frequency of 0.002 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: African in 1 of 14724 chromosomes (freq: 0.00007), Other in 14 of 4544 chromosomes (freq: 0.003), Latino in 18 of 24560 chromosomes (freq: 0.0007), European in 78 of 64948 chromosomes (freq: 0.001), Ashkenazi Jewish in 212 of 8190 chromosomes (freq: 0.03), and South Asian in 19 of 22622 chromosomes (freq: 0.0008), while the variant was not observed in the East Asian, and Finnish, populations. In addition we cannot be certain that data from control databases is specific to PKD1 and not from one of the six PKD1 pseudogenes. The p.Ser196= 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) 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.

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