dbSNP rs10823829: CDH23:p.Ser1003Ser (chr10-71706952-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_022124.6(CDH23):c.3009T>C(p.Ser1003Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 1,606,624 control chromosomes in the GnomAD database, including 10,081 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1003S) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.15 ( 3403 hom., cov: 33)

Exomes 𝑓: 0.055 ( 6678 hom. )

Consequence

CDH23
NM_022124.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -2.56

Publications

19 publications found

Variant links:

Genes affected

CDH23 (HGNC:13733): (cadherin related 23) This gene is a member of the cadherin superfamily, whose genes encode calcium dependent cell-cell adhesion glycoproteins. The encoded protein is thought to be involved in stereocilia organization and hair bundle formation. The gene is located in a region containing the human deafness loci DFNB12 and USH1D. Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of this cadherin-like gene. Upregulation of this gene may also be associated with breast cancer. Alternative splice variants encoding different isoforms have been described. [provided by RefSeq, May 2013]

CDH23 Gene-Disease associations (from GenCC):

autosomal recessive nonsyndromic hearing loss 12
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
nonsyndromic genetic hearing loss
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
Usher syndrome type 1D
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
Usher syndrome type 1
Inheritance: Unknown, AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
hearing loss, autosomal recessive
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CDH23 links:

ENSG00000300551 (HGNC:):

ENSG00000300551 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 10-71706952-T-C is Benign according to our data. Variant chr10-71706952-T-C is described in ClinVar as Benign. ClinVar VariationId is 44111.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.56 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022124.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CDH23	NM_022124.6	MANE Select	c.3009T>C	p.Ser1003Ser	synonymous	Exon 26 of 70	NP_071407.4
CDH23	NM_001171930.2		c.3009T>C	p.Ser1003Ser	synonymous	Exon 26 of 32	NP_001165401.1	A0A087WYR8
CDH23	NM_001171931.2		c.3009T>C	p.Ser1003Ser	synonymous	Exon 26 of 26	NP_001165402.1	Q8N5B3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CDH23	ENST00000224721.12	TSL:5 MANE Select	c.3009T>C	p.Ser1003Ser	synonymous	Exon 26 of 70	ENSP00000224721.9	Q9H251-1
CDH23	ENST00000616684.4	TSL:5	c.3009T>C	p.Ser1003Ser	synonymous	Exon 26 of 32	ENSP00000482036.2	A0A087WYR8
CDH23	ENST00000398809.9	TSL:5	c.3009T>C	p.Ser1003Ser	synonymous	Exon 26 of 32	ENSP00000381789.5	A0A0A0MS94

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22455

AN:

152116

Hom.:

3378

Cov.:

show subpopulations

Gnomad AFR

AF:

0.369

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.273

Gnomad SAS

AF:

0.0911

Gnomad FIN

AF:

0.0106

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0287

Gnomad OTH

AF:

0.130

GnomAD2 exomes

AF:

0.103

AC:

24322

AN:

235186

AF XY:

0.0936

show subpopulations

Gnomad AFR exome

AF:

0.373

Gnomad AMR exome

AF:

0.215

Gnomad ASJ exome

AF:

0.128

Gnomad EAS exome

AF:

0.254

Gnomad FIN exome

AF:

0.00880

Gnomad NFE exome

AF:

0.0305

Gnomad OTH exome

AF:

0.0791

GnomAD4 exome

AF:

0.0548

AC:

79771

AN:

1454390

Hom.:

6678

Cov.:

AF XY:

0.0548

AC XY:

39578

AN XY:

722732

show subpopulations

African (AFR)

AF:

0.371

AC:

12361

AN:

33310

American (AMR)

AF:

0.211

AC:

9162

AN:

43472

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

3330

AN:

25926

East Asian (EAS)

AF:

0.292

AC:

11468

AN:

39290

South Asian (SAS)

AF:

0.0957

AC:

8101

AN:

84668

European-Finnish (FIN)

AF:

0.0103

AC:

542

AN:

52804

Middle Eastern (MID)

AF:

0.122

AC:

705

AN:

5762

European-Non Finnish (NFE)

AF:

0.0263

AC:

29192

AN:

1109024

Other (OTH)

AF:

0.0817

AC:

4910

AN:

60134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

4369

8737

13106

17474

21843

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1514

3028

4542

6056

7570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.148

AC:

22539

AN:

152234

Hom.:

3403

Cov.:

AF XY:

0.145

AC XY:

10828

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.370

AC:

15334

AN:

41498

American (AMR)

AF:

0.166

AC:

2533

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

433

AN:

3472

East Asian (EAS)

AF:

0.272

AC:

1410

AN:

5178

South Asian (SAS)

AF:

0.0910

AC:

439

AN:

4826

European-Finnish (FIN)

AF:

0.0106

AC:

113

AN:

10632

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0287

AC:

1950

AN:

68018

Other (OTH)

AF:

0.130

AC:

275

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

881

1762

2643

3524

4405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0707

Hom.:

2889

Bravo

AF:

0.175

Asia WGS

AF:

0.173

AC:

604

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (4)

Autosomal recessive nonsyndromic hearing loss 12 (2)

not provided (2)

Usher syndrome type 1D (2)

Usher syndrome type 1 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.026

(source)

DANN

Benign

0.58

PhyloP100

-2.6

Mutation Taster

=87/13

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over