ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.11976C>G (p.Ala3992=) (rs112387277)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000252377 SCV000305687 likely benign not specified criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000712585 SCV000843101 benign not provided 2018-04-06 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001001863 SCV001159580 benign Polycystic kidney disease, adult type 2019-05-24 criteria provided, single submitter clinical testing
Molecular Genetics of Inherited Kidney Disorders Laboratory,Garvan Institute of Medical Research RCV001254184 SCV001430157 benign Autosomal dominant polycystic kidney disease 2019-01-01 criteria provided, single submitter research
GeneDx RCV000712585 SCV001817579 likely benign not provided 2020-12-18 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 10200984, 11967008, 10987650)
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001292420 SCV001480873 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Ala3992Ala variant was identified in 4 of 732 proband chromosomes (frequency: 0.005) from individuals or families with ADPKD (Badenas 1999, Perrichot 1999, Rossetti 2002). The variant was also identified in dbSNP (ID: rs112387277) as “With Likely benign allele”, Clinvitae (classified as likely benign), ClinVar (classified as likely benign by Prevention Genetics), ADPKD Mutation Database (classified as likely neutral), the 1000 Genomes Project in 4 of 5000 chromosomes (frequency: 0.0008), the NHLBI GO Exome Sequencing Project in 29 of 8486 European American and in 1 of 4288 African American alleles, the Exome Aggregation Consortium database (August 8th 2016) in 262 (1 homozygous) of 59468 chromosomes (freq. 0.004) in the following populations: European in 196 of 31204 chromosomes (freq. 0.006), Asian in 30 of 11894 chromosomes (freq. 0.003), Latino in 21 of 5190 chromosomes (freq. 0.004), Finnish in 8 of 2492 chromosomes (freq. 0.003), African in 7 of 4082 chromosomes (freq. 0.002), increasing the likelihood this could be a low frequency benign variant. The p.Ala3992Ala 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. 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 RCV000712585 SCV001932690 likely benign not provided no assertion criteria provided clinical testing

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