ClinVar Miner

Submissions for variant NM_003742.4(ABCB11):c.3556G>A (p.Glu1186Lys)

gnomAD frequency: 0.00943  dbSNP: rs1521808
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000176656 SCV000228347 other not provided 2018-05-02 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000254105 SCV000309815 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000254105 SCV000517791 benign not specified 2016-07-12 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.
Invitae RCV000176656 SCV001109056 benign not provided 2024-01-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001133697 SCV001293407 benign Progressive familial intrahepatic cholestasis type 2 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 rule this variant out of causing disease. Therefore, this variant is classified as benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000254105 SCV002103712 benign not specified 2022-02-18 criteria provided, single submitter clinical testing Variant summary: ABCB11 c.3556G>A (p.Glu1186Lys) results in a conservative amino acid change located in the ABC transporter-like, ATP-binding domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0021 in 249196 control chromosomes, predominantly at a frequency of 0.031 within the African or African-American subpopulation in the gnomAD database, including 4 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 13.86 fold of the estimated maximal expected allele frequency for a pathogenic variant in ABCB11 causing Familial Intrahepatic Cholestasis phenotype (0.0022), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
CeGaT Center for Human Genetics Tuebingen RCV000176656 SCV004183792 benign not provided 2023-12-01 criteria provided, single submitter clinical testing ABCB11: BS1, BS2
Natera, Inc. RCV001133697 SCV001458318 benign Progressive familial intrahepatic cholestasis type 2 2020-06-06 no assertion criteria provided clinical testing

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