ClinVar Miner

Submissions for variant NM_000527.5(LDLR):c.1617C>T (p.Pro539=) (rs5929)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
LDLR-LOVD, British Heart Foundation RCV000238018 SCV000295539 benign Familial hypercholesterolemia 1 2016-03-25 criteria provided, single submitter literature only
PreventionGenetics,PreventionGenetics RCV000243017 SCV000304686 benign not specified criteria provided, single submitter clinical testing
Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge RCV000238018 SCV000322964 benign Familial hypercholesterolemia 1 2016-03-01 criteria provided, single submitter research 8/95 non-FH individuals; MAF = 4,7% in 86 Spanish healthy individuals
Illumina Clinical Services Laboratory,Illumina RCV000238018 SCV000410535 benign Familial hypercholesterolemia 1 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.
GeneDx RCV000243017 SCV000525634 benign not specified 2016-10-21 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Color Health, Inc RCV000238018 SCV000689764 benign Familial hypercholesterolemia 1 2017-06-22 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589450 SCV000697205 benign not provided 2016-04-06 criteria provided, single submitter clinical testing Variant summary: This LDLR c.1617C>T variant affects a non-conserved nucleotide, resulting in synonymous amino acid change. 5/5 splice-site tools via Alamut predict that this variant does not affect normal splicing. This variant was found in 9229/121288 control chromosomes from the large and broad populations of ExAC at a frequency of 0.0760916 including several homozygotes, which is over 60 times greater than the maximal expected frequency of a pathogenic LDLR allele (0.0012508), suggesting this variant is benign. The variant has also been reported to co-occur with other potentially pathogenic variants such as c.68-1G>A (internal finding in one specimen), c.1634G>A (internal finding in one specimen), and p. p.Cys667Ser (Zakharova_2005), further supporting the benign outcome. Additionally, the variant is reported in the literature to be a common polymorphism that has no effect on plasma triglyceride, HDL cholesterol, apoA1 or lipoprotein (a) levels (Wu_Atheroscl_1999). Taken together, this variant has been classified as Benign.
Department of Human Genetics,Laborarztpraxis Dres. Walther, Weindel und Kollegen RCV000238018 SCV000987007 benign Familial hypercholesterolemia 1 2018-07-30 criteria provided, single submitter clinical testing Due to the increased occurrence of the mutation (>= 5%), this variant is classified as benign.
Invitae RCV001518851 SCV001727625 benign Familial hypercholesterolemia 2020-12-05 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV000238018 SCV001738000 benign Familial hypercholesterolemia 1 2021-06-10 criteria provided, single submitter clinical testing
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde,Academisch Medisch Centrum RCV000238018 SCV000606467 benign Familial hypercholesterolemia 1 no assertion criteria provided research
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000238018 SCV000733823 benign Familial hypercholesterolemia 1 no assertion criteria provided clinical testing
Natera, Inc. RCV001275280 SCV001460280 benign Smith-Lemli-Opitz syndrome 2020-09-16 no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000243017 SCV001919172 benign not specified no assertion criteria provided clinical testing

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