ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.5896C>T (p.Leu1966=) (rs1266923)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082564 SCV000114606 benign not specified 2013-04-23 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000082564 SCV000315815 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000314583 SCV000464077 benign Autosomal recessive polycystic kidney disease 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000082564 SCV000592898 benign not specified 2016-05-16 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589675 SCV000699870 benign not provided 2016-04-27 criteria provided, single submitter clinical testing Variant summary: The c.5896C>T variant involves the alteration of a 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 3.2%, predominantly observed in the African subpopulation at a frequency of 13.5% including 82 homozygous occurrences. This frequency exceeds the maximal expected allele frequency for a pathogenic variant in PKHD1 (0.71%), suggesting this is a benign polymorphism found primarily in population(s) of African origin. Publications and a clinical lab have classifed the variant as polymorphism/benign.
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000314583 SCV000743914 benign Autosomal recessive polycystic kidney disease 2014-12-01 criteria provided, single submitter clinical testing
Invitae RCV000314583 SCV000754662 benign Autosomal recessive polycystic kidney disease 2019-12-31 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000314583 SCV000734506 benign Autosomal recessive polycystic kidney disease no assertion criteria provided clinical testing

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