chr10-71799095-A-G

Variant names:

Variant summary

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

The NM_022124.6(CDH23):c.7055-16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 1,600,438 control chromosomes in the GnomAD database, including 81,703 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 9720 hom., cov: 32)

Exomes 𝑓: 0.31 ( 71983 hom. )

Consequence

CDH23
NM_022124.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -1.18

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:

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 (BayesDel_noAF=-0.86).

BP6

Variant 10-71799095-A-G is Benign according to our data. Variant chr10-71799095-A-G is described in ClinVar as [Benign]. Clinvar id is 46025.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-71799095-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CDH23	NM_022124.6 link	c.7055-16A>G	intron_variant	Intron 50 of 69	ENST00000224721.12	NP_071407.4	Q9H251-1Q6P152
CDH23	NM_001171933.1 link	c.335-16A>G	intron_variant	Intron 3 of 22		NP_001165404.1	Q9H251-7
CDH23	NM_001171934.1 link	c.335-16A>G	intron_variant	Intron 3 of 21		NP_001165405.1	Q9H251-9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH23	ENST00000224721.12 link	c.7055-16A>G		intron_variant	Intron 50 of 69	5	NM_022124.6	ENSP00000224721.9		Q9H251-1

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52480

AN:

151946

Hom.:

9700

Cov.:

show subpopulations

Gnomad AFR

AF:

0.444

Gnomad AMI

AF:

0.392

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.615

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.346

Gnomad MID

AF:

0.172

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.321

GnomAD3 exomes

AF:

0.341

AC:

83505

AN:

244856

Hom.:

15695

AF XY:

0.326

AC XY:

43319

AN XY:

132846

show subpopulations

Gnomad AFR exome

AF:

0.451

Gnomad AMR exome

AF:

0.444

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.622

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.349

Gnomad NFE exome

AF:

0.278

Gnomad OTH exome

AF:

0.304

GnomAD4 exome

AF:

0.305

AC:

441809

AN:

1448374

Hom.:

71983

Cov.:

AF XY:

0.301

AC XY:

216473

AN XY:

718976

show subpopulations

Gnomad4 AFR exome

AF:

0.450

Gnomad4 AMR exome

AF:

0.434

Gnomad4 ASJ exome

AF:

0.234

Gnomad4 EAS exome

AF:

0.664

Gnomad4 SAS exome

AF:

0.266

Gnomad4 FIN exome

AF:

0.346

Gnomad4 NFE exome

AF:

0.285

Gnomad4 OTH exome

AF:

0.313

GnomAD4 genome

AF:

0.345

AC:

52537

AN:

152064

Hom.:

9720

Cov.:

AF XY:

0.348

AC XY:

25861

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.444

Gnomad4 AMR

AF:

0.355

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.615

Gnomad4 SAS

AF:

0.280

Gnomad4 FIN

AF:

0.346

Gnomad4 NFE

AF:

0.274

Gnomad4 OTH

AF:

0.319

Alfa

AF:

0.294

Hom.:

1262

Bravo

AF:

0.358

Asia WGS

AF:

0.412

AC:

1434

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 12, 2009

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 27, 2017

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal recessive nonsyndromic hearing loss 12;C1832845:Usher syndrome type 1D;C4539685:Pituitary adenoma 5, multiple types

Benign:1

Apr 21, 2022

Fulgent Genetics, Fulgent Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Usher syndrome type 1D

Benign:1

Jul 01, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal recessive nonsyndromic hearing loss 12

Benign:1

Jul 01, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.072

DANN

Benign

0.28

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