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NM_022124.6(CDH23):c.6492C>T (p.Ile2164=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000046012.6
Variation ID:
46012
Description:
single nucleotide variant
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NM_022124.6(CDH23):c.6492C>T (p.Ile2164=)

Allele ID
55177
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71793420 (GRCh38) GRCh38 UCSC
10: 73553177 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73553177C>T
NC_000010.11:g.71793420C>T
NM_022124.6:c.6492C>T MANE Select NP_071407.4:p.Ile2164= synonymous
NG_008835.1:g.401474C>T
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:71793419:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.02616 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02335
Exome Aggregation Consortium (ExAC) 0.00685
1000 Genomes Project 0.02616
The Genome Aggregation Database (gnomAD) 0.02103
Trans-Omics for Precision Medicine (TOPMed) 0.02379
The Genome Aggregation Database (gnomAD), exomes 0.00570
Links
ClinGen: CA137537
dbSNP: rs41281332
VarSome
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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 Mar 16, 2017 RCV000039248.3
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV000965144.3
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV001104583.1
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV001104584.1
Benign 1 no assertion criteria provided Sep 16, 2020 RCV001274903.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CDH23 - - GRCh38
GRCh37
2166 2606

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 12
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001261460.1
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)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1D
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001261461.1
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)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001112404.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 16, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000731175.1
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
(Jan 10, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000062932.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Ile2164Ile in exon 48 of CDH23: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, … (more)
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 1
Allele origin: germline
Natera, Inc.
Accession: SCV001459456.1
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 rs41281332...

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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 07, 2021