ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.276G>A (p.Ala92=)

gnomAD frequency: 0.00354  dbSNP: rs374518168
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001000030 SCV000604760 benign Polycystic kidney disease, adult type 2020-04-06 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000712605 SCV000843122 benign not provided 2017-10-09 criteria provided, single submitter clinical testing
Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research RCV001254316 SCV001430268 benign Autosomal dominant polycystic kidney disease 2019-01-01 criteria provided, single submitter research
GeneDx RCV000712605 SCV001906527 benign not provided 2020-01-15 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 11857740, 11840199, 11316854, 22383692, 11115377)
Fulgent Genetics, Fulgent Genetics RCV001000030 SCV002806715 benign Polycystic kidney disease, adult type 2021-11-29 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000712605 SCV004142920 likely benign not provided 2024-11-01 criteria provided, single submitter clinical testing PKD1: BP4, BP7, BS2
Breakthrough Genomics, Breakthrough Genomics RCV000712605 SCV005290754 benign not provided criteria provided, single submitter not provided
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000502491 SCV000592729 benign not specified no assertion criteria provided clinical testing The PKD1 p.Ala92Ala variant was identified in 3 of 722 proband chromosomes (frequency: 0.004) from individuals or families with ADPKD (Rossetti 2001, Rossetti 2012). The variant was also identified in dbSNP (ID: rs374518168) as “NA” and in the 1000 Genomes Project in 20 of 5000 chromosomes (frequency: 0.004). The variant was also identified in the Exome Aggregation Consortium database (March 14, 2016) in 126 of 12248 chromosomes (frequency: 0.010) specifically in 3 in 188 (frequency: 0.016) Latino alleles, 90 in 7570 (frequency: 0.012) South Asians alleles including 3 homozygous individuals, 30 in 3556 (frequency: 0.008) European Non Finnish alleles, 1 in 578 (frequency: 0.002) African alleles, 2 in 134 (frequency: 0.015) other alleles, increasing the likelihood this could be a low frequency benign variant. In addition, the variant was listed in the GeneInsight COGR (1x benign) and in the ADPKD Mutation database (6x “Likely Neutral”). The p.Ala92Ala 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, this variant is classified as benign.

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