ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.11538-11C>T

gnomAD frequency: 0.00139  dbSNP: rs377692278
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000245054 SCV000305680 likely benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001001790 SCV001159441 benign Polycystic kidney disease, adult type 2019-01-06 criteria provided, single submitter clinical testing
GeneDx RCV001731462 SCV001983889 likely benign not provided 2021-04-19 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 10987650, 22383692, 17574468)
Fulgent Genetics, Fulgent Genetics RCV001001790 SCV002813194 likely benign Polycystic kidney disease, adult type 2021-08-03 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000245054 SCV003934691 benign not specified 2023-05-25 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292272 SCV001480931 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 c.11538-11C>T variant was identified in 5 of 916 proband chromosomes (frequency: 0.005) from French and North American individuals or families with ADPKD (Garcia-Gonzalez 2007, Perrichot 1999, Rossetti 2012). The variant was also identified in dbSNP (ID: rs377692278) “With Likely benign allele”, ClinVar (classified likely benign by Prevention Genetics), and ADPKD Mutation Database (as likely neutral), but was not identified in COGR, and PKD1-LOVD databases. The variant was identified in control databases in 286 of 199042 chromosomes at a frequency of 0.001 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). Breakdown of the observations by population include African in 8 of 18176 chromosomes (freq: 0.0004), European Non-Finnish in 223 of 188344 chromosomes (freq: 0.003), South Asian in 9 of 24676 chromosomes (freq: 0.0004), Other in 8 of 5104 chromosomes (freq: 0.002), Latino in 26 of 28456 chromosomes (freq: 0.0009), East Asian in 1 of 15360 chromosomes (freq: 0.00007), and European Finnish in 11 of 10842 chromosomes (freq: 0.001); it was not observed in the Ashkenazi Jewish population. The variant occurs outside of the splicing consensus sequence and 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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