ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.837G>A (p.Gly279=) (rs372124319)

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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 RCV000243779 SCV000305794 likely benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000999998 SCV000604746 benign Polycystic kidney disease, adult type 2020-02-03 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000243779 SCV000614548 benign not specified 2020-08-27 criteria provided, single submitter clinical testing
GeneDx RCV001610592 SCV001833434 benign not provided 2020-01-15 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001292511 SCV001480644 benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Gly279= variant was not identified in the literature nor was it identified in the LOVD 3.0 or PKD1-LOVD databases. The variant was identified in dbSNP (ID: rs372124319) as "With other allele", ClinVar (classified as benign by ARUP and Athena Diagnostics; as likely benign by Prevention Genetics), and in ADPKD Mutation Database (as Likely Neutral). The variant was identified in control databases in 1057 of 209002 chromosomes (16 homozygous) at a frequency of 0.005, increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 5 of 18078 chromosomes (freq: 0.0003), Other in 32 of 5288 chromosomes (freq: 0.006), Latino in 989 of 27992 chromosomes (freq: 0.04), European in 4 of 90316 chromosomes (freq: 0.00004), East Asian in 25 of 14370 chromosomes (freq: 0.002), and South Asian in 2 of 26106 chromosomes (freq: 0.00008), while the variant was not observed in the Ashkenazi Jewish or Finnish populations. 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.Gly279= 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. However, 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predicts a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information, this variant meets our laboratory criteria to be classified as benign.

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