Submissions for variant NM_000053.4(ATP7B):c.3101A>G (p.His1034Arg)

gnomAD frequency: 0.00430  dbSNP: rs74085882

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000244000	SCV000301715	benign	not specified		criteria provided, single submitter	clinical testing
GeneDx	RCV000244000	SCV000524982	benign	not specified	2017-05-11	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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000244000	SCV000602605	likely benign	not specified	2016-12-02	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000244000	SCV000694437	benign	not specified	2017-07-06	criteria provided, single submitter	clinical testing	Variant summary: The c.3101A>G (p.His1034Arg) in ATP7B gene is a missense change that involves a conserved nucleotide and 3/5 in silico tools predict benign outcome. The variant is present in the control population dataset of ExAC at frequency of 0.0012 (141/118116 chrs tested), predominantly in individuals of African descent (0.0143; 133/9302 chrs, including 3 homozygotes). The observed frequency exceeds the maximum expected allele frequency for a pathogenic variant in this gene (0.0054), suggesting that it is an ethnic benign polymorphism. The variant of interest has not, to our knowledge, been identified in affected individuals via published reports, but is cited as Benign/Likely Benign by reputable database/clinical laboratories. Taking together, based on the prevalence in general population the variant was classified as Benign.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000029368	SCV000752273	benign	Wilson disease	2025-02-03	criteria provided, single submitter	clinical testing
Mendelics	RCV000029368	SCV001139351	likely benign	Wilson disease	2019-05-28	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002321488	SCV002605921	likely benign	Inborn genetic diseases	2016-05-17	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
CeGaT Center for Human Genetics Tuebingen	RCV003390701	SCV004133154	likely benign	not provided	2023-10-01	criteria provided, single submitter	clinical testing	ATP7B: PM5, BS1, BS2
Color Diagnostics, LLC DBA Color Health	RCV000029368	SCV004361973	likely benign	Wilson disease	2022-09-29	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000029368	SCV004822716	likely benign	Wilson disease	2024-02-05	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV003390701	SCV005215653	likely benign	not provided		criteria provided, single submitter	not provided
CSER _CC_NCGL, University of Washington	RCV000029368	SCV000190071	uncertain significance	Wilson disease	2014-06-01	no assertion criteria provided	research
Natera, Inc.	RCV000029368	SCV001454155	benign	Wilson disease	2020-04-15	no assertion criteria provided	clinical testing