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NM_022124.6(CDH23):c.3431-6A>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 8, 2020
Accession:
VCV000227223.5
Variation ID:
227223
Description:
single nucleotide variant
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NM_022124.6(CDH23):c.3431-6A>T

Allele ID
229871
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71725366 (GRCh38) GRCh38 UCSC
10: 73485123 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73485123A>T
NC_000010.11:g.71725366A>T
NM_022124.6:c.3431-6A>T MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:71725365:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00025
1000 Genomes Project 0.00020
Exome Aggregation Consortium (ExAC) 0.00004
The Genome Aggregation Database (gnomAD), exomes 0.00005
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00020
Links
ClinGen: CA5544730
dbSNP: rs377614198
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter May 27, 2015 RCV000221627.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Oct 8, 2020 RCV000727019.4
Likely benign 1 no assertion criteria provided Sep 16, 2020 RCV001272886.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
C10orf105 - - - GRCh38
GRCh37
- 277
CDH23 - - GRCh38
GRCh37
2136 2571

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 19, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000704979.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(May 27, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000270036.2
Submitted: (Mar 21, 2019)
Evidence details
Comment:
c.3431-6A>T in intron 29 of CDH23: This variant is not expected to have clinical significance because a thymine "T" at this position does not diverge … (more)
Likely benign
(Oct 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001066185.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 1
Allele origin: germline
Natera, Inc.
Accession: SCV001455309.1
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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CDH23 - - - -

Text-mined citations for rs377614198...

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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