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NM_015404.4(WHRN):c.2644C>A (p.Arg882Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(5)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jul 20, 2021)
Last evaluated:
Feb 3, 2021
Accession:
VCV000194094.6
Variation ID:
194094
Description:
single nucleotide variant
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NM_015404.4(WHRN):c.2644C>A (p.Arg882Ser)

Allele ID
191257
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q32
Genomic location
9: 114402834 (GRCh38) GRCh38 UCSC
9: 117165114 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.117165114G>T
NC_000009.12:g.114402834G>T
NM_015404.4:c.2644C>A MANE Select NP_056219.3:p.Arg882Ser missense
... more HGVS
Protein change
R882S, R499S, R881S, R531S
Other names
-
Canonical SPDI
NC_000009.12:114402833:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00094
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00138
Links
ClinGen: CA239906
dbSNP: rs150586098
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 Mar 18, 2019 RCV000174376.3
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001165659.1
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001165660.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Feb 3, 2021 RCV000724279.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
WHRN - - GRCh38
GRCh37
447 487

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 19, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000225665.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Mar 18, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000603296.2
Submitted: (Aug 05, 2019)
Evidence details
Comment:
The WHRN c.2644C>A; p.Arg882Ser variant (rs150586098; ClinVar Variation ID: 194094) is found in the general population with an overall allele frequency of 0.04% (112/281,334 alleles) … (more)
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001060543.2
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Feb 03, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001757710.1
Submitted: (Jul 20, 2021)
Evidence details
Comment:
Observed in cis with S648Y in unrelated individuals in the published literature and at GeneDx (Aller et al., 2010; Audo et al., 2012); In silico … (more)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 31
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001327876.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001327877.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (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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Title Author Journal Year Link
Sequence variants of the DFNB31 gene among Usher syndrome patients of diverse origin. Aller E Molecular vision 2010 PMID: 20352026
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=WHRN - - - -

Text-mined citations for rs150586098...

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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 Aug 17, 2021