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NM_006005.3(WFS1):c.2667G>A (p.Ala889=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jul 4, 2021)
Last evaluated:
Nov 10, 2020
Accession:
VCV000166614.11
Variation ID:
166614
Description:
single nucleotide variant
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NM_006005.3(WFS1):c.2667G>A (p.Ala889=)

Allele ID
173843
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
4p16.1
Genomic location
4: 6302462 (GRCh38) GRCh38 UCSC
4: 6304189 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000004.11:g.6304189G>A
NC_000004.12:g.6302462G>A
NM_006005.3:c.2667G>A MANE Select NP_005996.2:p.Ala889= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000004.12:6302461:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00010
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD), exomes 0.00032
Exome Aggregation Consortium (ExAC) 0.00035
Trans-Omics for Precision Medicine (TOPMed) 0.00014
Links
ClinGen: CA179687
dbSNP: rs71526454
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Mar 13, 2018 RCV000152702.3
Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 10, 2020 RCV000864405.4
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001156288.1
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV001157955.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
WFS1 No evidence available No evidence available GRCh38
GRCh37
757 832

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Mar 13, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000515281.4
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)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
WFS1-Related Spectrum Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001319564.1
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)
Likely benign
(Nov 10, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001005201.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Sep 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001249100.5
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(Aug 19, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000202084.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Ala889Ala in exon 8 of WFS1: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Autosomal dominant nonsyndromic deafness 6
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001317776.1
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)

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 rs71526454...

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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 Jul 10, 2021