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

gnomAD frequency: 0.00161  dbSNP: rs148852027

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	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	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
CeGaT Center for Human Genetics Tuebingen	RCV000712627	SCV004142878	likely benign	not provided	2023-03-01	criteria provided, single submitter	clinical testing	PKD1: BP4, BP7
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
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000712627	SCV001972751	likely benign	not provided		no assertion criteria provided	clinical testing