ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.5847C>T (p.Ser1949=) (rs80111665)

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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 RCV000248114 SCV000305758 likely benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000999978 SCV000604805 benign Polycystic kidney disease, adult type 2019-01-29 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000712636 SCV000843153 benign not provided 2018-03-21 criteria provided, single submitter clinical testing
GeneDx RCV000712636 SCV001900991 benign not provided 2020-10-14 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 11012875, 22383692, 18837007, 22185115)
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001292412 SCV001480841 benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Ser1949= variant was identified in 1 of 460 proband chromosomes (frequency: 0.002) from individuals or families with ADPKD, and was present in 1 of 92 control chromosomes (frequency: 0.01) from healthy individuals (Rossetti_2012_22383692, Phakdeekitcharoen_2000_11012875). The variant was also identified in dbSNP (ID: rs80111665) as “With Likely benign allele”, ClinVar (classified as benign by ARUP Laboratories and likely benign by PreventionGenetics), and the ADPKD Mutation Database (classified as likely neutral). The variant was not identified in GeneInsight-COGR, LOVD 3.0, or PKD1-LOVD databases. The variant was identified in control databases in 1665 of 257370 chromosomes (38 homozygous) at a frequency of 0.006 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include African in 3 of 22624 chromosomes (freq: 0.0001), Other in 41 of 6190 chromosomes (freq: 0.007), Latino in 112 of 33994 chromosomes (freq: 0.003), European Non-Finnish in 123 of 119088 chromosomes (freq: 0.001), Ashkenazi Jewish in 53 of 9568 chromosomes (freq: 0.006), East Asian in 1005 of 18588 chromosomes (freq: 0.05), European Finnish in 280 of 17560 chromosomes (freq: 0.02), and South Asian in 48 of 29758 chromosomes (freq: 0.002). 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 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; this is not very predictive of pathogenicity. The p.Ser1949= 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 summary, based on the above information this variant meets our laboratory criteria to be classified as benign.

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