Variant 10-71397276-C-CCGAGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_022124.6(CDH23):c.-35_-31dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 13441 hom., cov: 0)

Exomes 𝑓: 0.40 ( 2201 hom. )

Consequence

CDH23
NM_022124.6 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.0300

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 -16 ACMG points.

BP6

Variant 10-71397276-C-CCGAGG is Benign according to our data. Variant chr10-71397276-C-CCGAGG is described in ClinVar as [Likely_benign]. Clinvar id is 300394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH23	NM_022124.6 linkuse as main transcript	c.-35_-31dup		5_prime_UTR_variant	1/70	ENST00000224721.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH23	ENST00000224721.12 linkuse as main transcript	c.-35_-31dup		5_prime_UTR_variant	1/70	5	NM_022124.6	P1	Q9H251-1

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

56853

AN:

150148

Hom.:

13447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0937

Gnomad AMI

AF:

0.497

Gnomad AMR

AF:

0.378

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.515

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.511

Gnomad OTH

AF:

0.379

GnomAD3 exomes

AF:

0.394

AC:

AN:

246

Hom.:

AF XY:

0.387

AC XY:

AN XY:

142

show subpopulations

Gnomad SAS exome

AF:

0.00

Gnomad NFE exome

AF:

0.406

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.400

AC:

8999

AN:

22518

Hom.:

2201

Cov.:

AF XY:

0.391

AC XY:

5554

AN XY:

14208

show subpopulations

Gnomad4 AFR exome

AF:

0.117

Gnomad4 AMR exome

AF:

0.286

Gnomad4 ASJ exome

AF:

0.373

Gnomad4 EAS exome

AF:

0.417

Gnomad4 SAS exome

AF:

0.332

Gnomad4 FIN exome

AF:

0.441

Gnomad4 NFE exome

AF:

0.442

Gnomad4 OTH exome

AF:

0.364

GnomAD4 genome

AF:

0.378

AC:

56835

AN:

150254

Hom.:

13441

Cov.:

AF XY:

0.381

AC XY:

27901

AN XY:

73326

show subpopulations

Gnomad4 AFR

AF:

0.0936

Gnomad4 AMR

AF:

0.378

Gnomad4 ASJ

AF:

0.440

Gnomad4 EAS

AF:

0.515

Gnomad4 SAS

AF:

0.406

Gnomad4 FIN

AF:

0.544

Gnomad4 NFE

AF:

0.511

Gnomad4 OTH

AF:

0.377

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Outside ROI, common in our data set -

CDH23-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Nonsyndromic Hearing Loss, Recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2020

- -

Retinitis pigmentosa-deafness syndrome

Benign:1

Likely 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

Splicing

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