rs45583140

Positions:

chr10-71812008-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022124.6(CDH23):c.9373T>C(p.Phe3125Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0501 in 1,612,768 control chromosomes in the GnomAD database, including 3,770 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.045 ( 328 hom., cov: 33)

Exomes 𝑓: 0.051 ( 3442 hom. )

Consequence

CDH23
NM_022124.6 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:18O:1

Conservation

PhyloP100: 5.75

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 links:

CDH23 (HGNC:):

CDH23 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0020181537).

BP6

Variant 10-71812008-T-C is Benign according to our data. Variant chr10-71812008-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 46072.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-71812008-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH23	NM_022124.6 linkuse as main transcript	c.9373T>C	p.Phe3125Leu	missense_variant	66/70	ENST00000224721.12	NP_071407.4	Q9H251-1Q6P152

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDH23	ENST00000224721.12 linkuse as main transcript	c.9373T>C	p.Phe3125Leu	missense_variant	66/70	5	NM_022124.6	ENSP00000224721.9		Q9H251-1

Frequencies

GnomAD3 genomes

AF:

0.0453

AC:

6853

AN:

151384

Hom.:

328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00978

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0726

Gnomad ASJ

AF:

0.0464

Gnomad EAS

AF:

0.248

Gnomad SAS

AF:

0.0917

Gnomad FIN

AF:

0.0943

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.0352

Gnomad OTH

AF:

0.0421

GnomAD3 exomes

AF:

0.0739

AC:

18420

AN:

249186

Hom.:

1180

AF XY:

0.0702

AC XY:

9496

AN XY:

135202

show subpopulations

Gnomad AFR exome

AF:

0.00949

Gnomad AMR exome

AF:

0.129

Gnomad ASJ exome

AF:

0.0466

Gnomad EAS exome

AF:

0.251

Gnomad SAS exome

AF:

0.0795

Gnomad FIN exome

AF:

0.0930

Gnomad NFE exome

AF:

0.0358

Gnomad OTH exome

AF:

0.0574

GnomAD4 exome

AF:

0.0506

AC:

73952

AN:

1461266

Hom.:

3442

Cov.:

AF XY:

0.0506

AC XY:

36816

AN XY:

726924

show subpopulations

Gnomad4 AFR exome

AF:

0.00720

Gnomad4 AMR exome

AF:

0.125

Gnomad4 ASJ exome

AF:

0.0469

Gnomad4 EAS exome

AF:

0.277

Gnomad4 SAS exome

AF:

0.0769

Gnomad4 FIN exome

AF:

0.0898

Gnomad4 NFE exome

AF:

0.0367

Gnomad4 OTH exome

AF:

0.0587

GnomAD4 genome

AF:

0.0452

AC:

6852

AN:

151502

Hom.:

328

Cov.:

AF XY:

0.0501

AC XY:

3710

AN XY:

74014

show subpopulations

Gnomad4 AFR

AF:

0.00975

Gnomad4 AMR

AF:

0.0725

Gnomad4 ASJ

AF:

0.0464

Gnomad4 EAS

AF:

0.248

Gnomad4 SAS

AF:

0.0920

Gnomad4 FIN

AF:

0.0943

Gnomad4 NFE

AF:

0.0351

Gnomad4 OTH

AF:

0.0427

Alfa

AF:

0.0403

Hom.:

399

Bravo

AF:

0.0444

TwinsUK

AF:

0.0383

AC:

142

ALSPAC

AF:

0.0394

AC:

152

ESP6500AA

AF:

0.0106

AC:

ESP6500EA

AF:

0.0326

AC:

271

ExAC

AF:

0.0696

AC:

8411

Asia WGS

AF:

0.167

AC:

580

AN:

3478

EpiCase

AF:

0.0346

EpiControl

AF:

0.0324

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:18Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3Other:1

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
not provided, no classification provided	literature only	NEI Ophthalmic Genomics Laboratory, National Institutes of Health	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 08, 2023	- -

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 02, 2013	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 a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 12, 2009	- -

Usher syndrome type 1D

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 01, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	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. -

Retinitis pigmentosa-deafness syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -

Autosomal recessive nonsyndromic hearing loss 12

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 01, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	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. -

Atypical Gaucher Disease

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Combined PSAP deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Usher syndrome type 1

Benign:1

Benign, no assertion criteria provided

clinical testing

Natera, Inc.

Sep 16, 2020

- -

Galactosylceramide beta-galactosidase deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Hearing loss, autosomal recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Metachromatic leukodystrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.95

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.26

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.013

T;T;.;.

Eigen

Uncertain

0.51

Eigen_PC

Uncertain

0.57

FATHMM_MKL

Benign

0.59

LIST_S2

Uncertain

0.87

D;D;D;D

MetaRNN

Benign

0.0020

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.8

.;L;.;.

PrimateAI

Pathogenic

0.84

PROVEAN

Benign

-0.38

.;.;.;N

REVEL

Benign

0.11

Sift

Benign

0.094

.;.;.;T

Sift4G

Uncertain

0.011

D;.;D;D

Polyphen

0.90

.;P;.;.

Vest4

0.66

MutPred

0.60

Loss of stability (P = 0.1003);Loss of stability (P = 0.1003);.;.;

MPC

0.17

ClinPred

0.015

GERP RS

5.8

Varity_R

0.45

gMVP

0.68

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over