NM_022124.6(CDH23):c.3009T>C (p.Ser1003=) AND Deafness, autosomal recessive 12

Clinical significance:Benign (Last evaluated: Jul 1, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_022124.6(CDH23):c.3009T>C (p.Ser1003=)]

NM_022124.6(CDH23):c.3009T>C (p.Ser1003=)

CDH23:cadherin related 23 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_022124.6(CDH23):c.3009T>C (p.Ser1003=)
Other names:
  • NC_000010.11:g.71706952T>C
  • NG_008835.1:g.315006T>C
  • NM_001171930.2:c.3009T>C
  • NM_001171931.2:c.3009T>C
  • NM_022124.6:c.3009T>CMANE SELECT
  • NP_001165401.1:p.Ser1003=
  • NP_001165402.1:p.Ser1003=
  • NP_071407.4:p.Ser1003=
  • NC_000010.10:g.73466709T>C
  • NM_001171931.1:c.3009T>C
  • NM_022124.5:c.3009T>C
  • c.3009T>C
  • p.Ser1003Ser
dbSNP: rs10823829
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001171930.2:c.3009T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001171931.2:c.3009T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_022124.6:c.3009T>C - synonymous variant - [Sequence Ontology: SO:0001819]


Deafness, autosomal recessive 12 (DFNB12)
MONDO: MONDO:0011067; MedGen: C1832394; Orphanet: 90636; OMIM: 601386

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000363675Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
(Jan 12, 2018)
germlineclinical testing

Citation Link,

SCV001750563Nilou-Genome Labcriteria provided, single submitter
(Jul 1, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing



Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000363675.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Nilou-Genome Lab, SCV001750563.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 16, 2021

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