ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.8247G>A (p.Ala2749=)

gnomAD frequency: 0.00080  dbSNP: rs143265128
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000507781 SCV000604799 benign not specified 2017-01-29 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000507781 SCV000614543 benign not specified 2016-10-20 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001796084 SCV004142840 likely benign not provided 2023-10-01 criteria provided, single submitter clinical testing PKD1: BP4, BP7
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292334 SCV001480638 benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Ala2749= variant was identified in 2 of 1044 proband chromosomes (frequency: 0.002) from individuals or families with ADPKD (Carrera 2016, Garcia-Gonzalez 2007). The variant was also identified in dbSNP (ID: rs143265128) as “NA”, the ADPKD Mutation Database (likely neurtal), in the 1000 Genomes Project (freq. 0.0008), the ESP Project in the European population (freq. 0.002), in the genome aggregation consortium (freq 0.0008) an in the Exome Aggregation Consortium database (August 8th 2016) in 80 of 112864 chromosomes (freq. 0.0007) in the following populations: Latino in 18 of 11034 chromosomes (freq. 0.002), Other in 1 of 828 chromosomes (freq. 0.001), European (Non-Finnish) in 53 of 61588 chromosomes (freq. 0.0009), African in 6 of 8872 chromosomes (freq. 0.0007), and South Asian in 2 of 16114 chromosomes (freq. 0.0001), but was not seen in East Asian or Finish populations, increasing the likelihood this could be a low frequency benign variant. 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.Ala2749= 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. The variant was identified by our laboratory in a patient with ADPKD with a co-occurring pathogenic PKD1 variant (p.Gln739X), increasing the likelihood that the p.Ala2749= variant does not have clinical significance. In summary, based on the above information, this variant meets our laboratory criteria to be classified as benign.
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV001796084 SCV002033939 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001796084 SCV002037822 likely benign not provided no assertion criteria provided clinical testing

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