ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.4917C>T (p.Gly1639=) (rs148852027)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000246928 SCV000305746 likely benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000999844 SCV000604772 benign Polycystic kidney disease, adult type 2020-02-27 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000712627 SCV000843144 benign not provided 2018-05-29 criteria provided, single submitter clinical testing
GeneDx RCV000712627 SCV001825666 likely benign not provided 2021-03-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001292395 SCV001480872 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Gly1639= variant was not identified in the literature nor was it identified in the databases GeneInsight-COGR or PKD1-LOVD. The variant was identified in dbSNP (ID: rs148852027) as "With Likely benign allele", ClinVar (2x, likely benign), Clinvitae, LOVD 3.0 (1x), and the ADPKD Mutation Database (likely neutral). The variant was identified in control databases in 387 of 271600 chromosomes at a frequency of 0.001 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 7 of 23132 chromosomes (freq: 0.0003), Other in 11 of 6314 chromosomes (freq: 0.002), Latino in 53 of 34320 chromosomes (freq: 0.002), European in 298 of 123000 chromosomes (freq: 0.002), Ashkenazi Jewish in 3 of 10006 chromosomes (freq: 0.0003), Finnish in 5 of 25308 chromosomes (freq: 0.0002), and South Asian in 10 of 30744 chromosomes (freq: 0.0003). The variant was not observed in the East Asian population. 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.Gly1639= 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 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.
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000246928 SCV001929836 benign not specified no assertion criteria provided clinical testing

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