ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.5725C>T (p.Arg1909Trp) (rs115338476)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082561 SCV000114603 benign not specified 2013-04-15 criteria provided, single submitter clinical testing
Counsyl RCV000169055 SCV000220215 likely benign Autosomal recessive polycystic kidney disease 2014-04-09 criteria provided, single submitter literature only
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224204 SCV000281597 likely benign not provided 2015-10-29 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Invitae RCV000169055 SCV000291336 benign Autosomal recessive polycystic kidney disease 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000082561 SCV000315814 benign not specified criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000224204 SCV000699868 likely benign not provided 2016-04-26 criteria provided, single submitter clinical testing Variant summary: The c.5725C>T variant involves the alteration of a non-conserved nucleotide and 3/4 in silico tools predict a benign outcome. The variant was observed in the large and broad cohorts of the ExAC project at an allele frequency of 0.18%, predominantly observed in the African subpopulation at a frequency of 1.8% including 2 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 Likely Benign. Taken together, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000169055 SCV001323631 likely benign Autosomal recessive polycystic kidney disease 2017-04-28 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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