ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.5373C>T (p.Asn1791=)

gnomAD frequency: 0.00357  dbSNP: rs143017410
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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 RCV000247927 SCV000305752 benign not specified criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000992587 SCV001144989 benign not provided 2019-05-10 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001002155 SCV001160010 benign Polycystic kidney disease, adult type 2018-10-01 criteria provided, single submitter clinical testing
GeneDx RCV000992587 SCV001901154 benign not provided 2020-06-29 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 22383692)
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292196 SCV001480920 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Asn1791= variant was identified in 2 of 550 proband chromosomes (frequency: 0.003636) from individuals or families with autosomal dominant polycystic kidney disease (ADPKD) (Rossetti 2002, Rossetti 2012). The variant was also identified in dbSNP (ID: rs143017410) “With Benign allele,” ClinVar (as benign by Prevention Genetics), and ADPKD Mutation Database (2x as likely neutral). The variant was not identified in GeneInsight-COGR, LOVD 3.0, and PKD1-LOVD databases. The variant was identified in control databases in 265 of 269328 chromosomes at a frequency of 0.001 increasing the likelihood that this may be a low frequency benign variant in certain populations of origin (Genome Aggregation Consortium Feb 27, 2017), being identified in the following populations: African in 234 of 22952 chromosomes (frequency: 0.0102), Ashkenazi Jewish in 6 of 9984 chromosomes (frequency: 0.00006), Latino in 20 of 34170 chromosomes (frequency: 0.00006), Other in 2 of 6290 chromosomes (frequency: 0.00003), and European Non-Finnish in 3 of 122142 chromosomes (frequency: 0.00002). 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.Asn1791= 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 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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