Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_022124.6(CDH23):c.7467C>T (p.Arg2489=)

Help
Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Jul 14, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000046031.8
Variation ID:
46031
Description:
single nucleotide variant
Help

NM_022124.6(CDH23):c.7467C>T (p.Arg2489=)

Allele ID
55196
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71800740 (GRCh38) GRCh38 UCSC
10: 73560497 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73560497C>T
NM_022124.6:c.7467C>T MANE Select NP_071407.4:p.Arg2489= synonymous
NM_001171932.1:c.*183260C>T
... more HGVS
Protein change
-
Other names
p.R2489R:CGC>CGT
Canonical SPDI
NC_000010.11:71800739:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.03974 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.01211
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01286
The Genome Aggregation Database (gnomAD) 0.01824
Trans-Omics for Precision Medicine (TOPMed) 0.02212
1000 Genomes Project 0.03974
Exome Aggregation Consortium (ExAC) 0.01281
Links
ClinGen: CA137569
dbSNP: rs111033289
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Apr 8, 2013 RCV000039267.5
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jul 1, 2021 RCV000285813.3
Benign 2 criteria provided, multiple submitters, no conflicts Jul 1, 2021 RCV000377904.3
Benign 1 criteria provided, single submitter Nov 21, 2019 RCV001282328.2
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV001511045.1
Benign 1 no assertion criteria provided Sep 16, 2020 RCV001274912.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CDH23 - - GRCh38
GRCh37
2166 2606

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Apr 08, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167623.10
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
(Sep 12, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000062951.5
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Arg2489Arg in exon 53 of CDH23: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, … (more)
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001750580.1
Submitted: (Jul 14, 2021)
Evidence details
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001750581.1
Submitted: (Jul 14, 2021)
Evidence details
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000363864.3
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000363863.3
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
(Nov 21, 2019)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001156998.2
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001718225.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 1
Allele origin: germline
Natera, Inc.
Accession: SCV001459465.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
Mutation profile of the CDH23 gene in 56 probands with Usher syndrome type I. Oshima A Human mutation 2008 PMID: 18429043

Text-mined citations for rs111033289...

Help
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 20, 2021