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NM_000053.4(ATP7B):c.1947-4C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Oct 12, 2021)
Last evaluated:
Aug 10, 2021
Accession:
VCV000387748.8
Variation ID:
387748
Description:
single nucleotide variant
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NM_000053.4(ATP7B):c.1947-4C>T

Allele ID
373861
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q14.3
Genomic location
13: 51960326 (GRCh38) GRCh38 UCSC
13: 52534462 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.11:g.51960326G>A
NG_008806.1:g.56169C>T
NM_001243182.2:c.1614-4C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000013.11:51960325:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00007
Trans-Omics for Precision Medicine (TOPMed) 0.00016
Exome Aggregation Consortium (ExAC) 0.00080
The Genome Aggregation Database (gnomAD), exomes 0.00064
The Genome Aggregation Database (gnomAD) 0.00013
Trans-Omics for Precision Medicine (TOPMed) 0.00026
1000 Genomes Project 0.00180
Links
ClinGen: CA6989146
dbSNP: rs74904335
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Oct 5, 2017 RCV000440735.3
Likely benign 1 criteria provided, single submitter Sep 11, 2018 RCV001721333.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Aug 10, 2021 RCV000631244.6
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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
Uncertain significance
(Oct 05, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000918584.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: The ATP7B c.1947-4C>T variant causes a missense change involving the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a damaging outcome for … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001267852.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Invitae
Accession: SCV000752268.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Sep 11, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000529873.5
Submitted: (Sep 30, 2021)
Evidence details
Likely benign
(Aug 10, 2021)
criteria provided, single submitter
Method: clinical testing
Wilson disease
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001977177.1
Submitted: (Oct 12, 2021)
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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Title Author Journal Year Link
Mutational analysis of ATP7B and genotype-phenotype correlation in Japanese with Wilson's disease. Okada T Human mutation 2000 PMID: 10790207
Identification of three novel mutations and a high frequency of the Arg778Leu mutation in Korean patients with Wilson disease. Kim EK Human mutation 1998 PMID: 9554743

Text-mined citations for rs74904335...

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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