Submissions for variant NM_000053.4(ATP7B):c.3419T>C (p.Val1140Ala)

gnomAD frequency: 0.57256  dbSNP: rs1801249

Total submissions: 20

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000078051	SCV000109889	benign	not specified	2017-10-19	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000078051	SCV000301718	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000029369	SCV000384654	benign	Wilson disease	2018-03-06	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	RCV000078051	SCV000517538	benign	not specified	2016-01-05	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	RCV000029369	SCV000602585	benign	Wilson disease	2022-03-08	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000029369	SCV001720713	benign	Wilson disease	2025-02-04	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000029369	SCV001750114	benign	Wilson disease	2021-07-01	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002453268	SCV002617906	benign	Inborn genetic diseases	2016-07-01	criteria provided, single submitter	clinical testing	This alteration is classified as 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.
Color Diagnostics, LLC DBA Color Health	RCV000029369	SCV004361964	benign	Wilson disease	2018-03-05	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000029369	SCV004845361	benign	Wilson disease	2024-10-03	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV001354257	SCV005230363	benign	not provided		criteria provided, single submitter	not provided
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000029369	SCV000052017	benign	Wilson disease	2011-11-26	no assertion criteria provided	clinical testing
Genetic Services Laboratory, University of Chicago	RCV000078051	SCV000192345	likely benign	not specified		no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000029369	SCV000733356	benign	Wilson disease		no assertion criteria provided	clinical testing
Natera, Inc.	RCV000029369	SCV001455589	benign	Wilson disease	2020-09-16	no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001354257	SCV001548824	uncertain significance	not provided		no assertion criteria provided	clinical testing	multiple AR variants in same gene - keep for nowAllele frequency is common in at least one population database (frequency: 64.181% in ExAC) based on the frequency threshold of 2.434% for this gene.Variant was observed in a homozygous state in population databases more than expected for disease.
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000078051	SCV001809783	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000078051	SCV001917240	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000078051	SCV001928628	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000078051	SCV001957444	benign	not specified		no assertion criteria provided	clinical testing