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

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000035719.8
Variation ID:
35719
Description:
single nucleotide variant
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NM_000053.4(ATP7B):c.3101A>G (p.His1034Arg)

Allele ID
44383
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q14.3
Genomic location
13: 51944251 (GRCh38) GRCh38 UCSC
13: 52518387 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.11:g.51944251T>C
NG_008806.1:g.72244A>G
NM_000053.4:c.3101A>G MANE Select NP_000044.2:p.His1034Arg missense
... more HGVS
Protein change
H1034R, H827R, H923R, H956R, H950R
Other names
-
Canonical SPDI
NC_000013.11:51944250:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00339 (C)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00119
The Genome Aggregation Database (gnomAD) 0.00357
The Genome Aggregation Database (gnomAD), exomes 0.00096
Trans-Omics for Precision Medicine (TOPMed) 0.00397
Trans-Omics for Precision Medicine (TOPMed) 0.00442
1000 Genomes Project 0.00339
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00360
The Genome Aggregation Database (gnomAD) 0.00430
Links
ClinGen: CA260138
dbSNP: rs74085882
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Dec 7, 2020 RCV000029368.10
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Jul 6, 2017 RCV000244000.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATP7B - - GRCh38
GRCh37
1325 1389

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000301715.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Dec 02, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000602605.1
Submitted: (Jun 30, 2017)
Evidence details
Benign
(May 11, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000524982.2
Submitted: (Mar 26, 2018)
Evidence details
Comment:
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 … (more)
Benign
(Jul 06, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694437.2
Submitted: (Apr 11, 2018)
Evidence details
Comment:
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. … (more)
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: unknown
Mendelics
Accession: SCV001139351.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Invitae
Accession: SCV000752273.4
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jun 01, 2014)
no assertion criteria provided
Method: research
Wilson disease
(Autosomal recessive inheritance)
Allele origin: germline
CSER _CC_NCGL, University of Washington
Study: ESP 6500 variant annotation
Accession: SCV000190071.1
Submitted: (Aug 28, 2014)
Comment:
Variants classified for the Actionable exomic incidental findings in 6503 participants: challenges of variant classification manuscript
Evidence details
Benign
(Apr 15, 2020)
no assertion criteria provided
Method: clinical testing
Wilson disease
Allele origin: germline
Natera, Inc.
Accession: SCV001454155.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs74085882...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021