ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.5199C>A (p.Thr1733=)

dbSNP: rs148790132
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001081150 SCV000291335 benign Autosomal recessive polycystic kidney disease 2024-01-31 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000245485 SCV000315809 benign not specified criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000245485 SCV000331172 benign not specified 2015-07-09 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589570 SCV000699867 benign not provided 2016-04-26 criteria provided, single submitter clinical testing Variant summary: The c.5199C>A variant involves the alteration of a non-conserved nucleotide resulting in a synonymous change. 4/5 in silico tools via Alamut predict no significant effect on splicing. The variant was observed in the large and broad cohorts of the ExAC project at an allele frequency of 0.50%, predominantly observed in the African subpopulation at a frequency of 5.2% including 14 homozygous occurrences. This frequency exceeds the maximal expected allele frequency for a pathogenic variant in PKHD1 (0.70%), suggesting this is a benign polymorphism found primarily in population(s) of African origin. One reputable clinical lab has classified the variant as "benign" and multiple publications consider the variant to be a polymorphism. Taken together, this variant has been classified as Benign.
Illumina Laboratory Services, Illumina RCV001081150 SCV001325284 benign Autosomal recessive polycystic kidney disease 2017-11-14 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
GeneDx RCV000589570 SCV001889335 benign not provided 2018-07-14 criteria provided, single submitter clinical testing
Natera, Inc. RCV001081150 SCV002078090 benign Autosomal recessive polycystic kidney disease 2017-06-30 no assertion criteria provided clinical testing

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