NM_022124.6:c.1753-43T>C

Variant names:

• chr10-71679344-T-C
• rs1227042
• NM_022124.6:c.1753-43T>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_022124.6(CDH23):​c.1753-43T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.959 in 1,317,136 control chromosomes in the GnomAD database, including 606,967 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.93 (65792 hom., cov: 33)
  • Exomes 𝑓: 0.96 (541175 hom.)
• Consequence: CDH23 NM_022124.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -1.81

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 10-71679344-T-C is Benign according to our data. Variant chr10-71679344-T-C is described in ClinVar as [Benign]. Clinvar id is 261543.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-71679344-T-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH23	NM_022124.6	c.1753-43T>C		intron_variant	Intron 16 of 69	ENST00000224721.12	NP_071407.4
CDH23	NM_001171930.2	c.1753-43T>C		intron_variant	Intron 16 of 31		NP_001165401.1
CDH23	NM_001171931.2	c.1753-43T>C		intron_variant	Intron 16 of 25		NP_001165402.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH23	ENST00000224721.12	c.1753-43T>C		intron_variant	Intron 16 of 69	5	NM_022124.6	ENSP00000224721.9

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141106 AN: 152108 Hom.: 65756 Cov.: 33

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.941

GnomAD3 exomes AF: 0.955 AC: 204806 AN: 214356 Hom.: 98118 AF XY: 0.962 AC XY: 111497 AN XY: 115870

Gnomad AFR exome AF: 0.832

Gnomad AMR exome AF: 0.875

Gnomad ASJ exome AF: 0.996

Gnomad EAS exome AF: 0.998

Gnomad SAS exome AF: 0.996

Gnomad FIN exome AF: 0.991

Gnomad NFE exome AF: 0.967

Gnomad OTH exome AF: 0.958

GnomAD4 exome AF: 0.963 AC: 1122227 AN: 1164910 Hom.: 541175 Cov.: 15 AF XY: 0.965 AC XY: 569549 AN XY: 589956

Gnomad4 AFR exome AF: 0.837

Gnomad4 AMR exome AF: 0.874

Gnomad4 ASJ exome AF: 0.997

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.995

Gnomad4 FIN exome AF: 0.991

Gnomad4 NFE exome AF: 0.964

Gnomad4 OTH exome AF: 0.960

GnomAD4 genome AF: 0.928 AC: 141198 AN: 152226 Hom.: 65792 Cov.: 33 AF XY: 0.930 AC XY: 69229 AN XY: 74440

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.997

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.941

Alfa AF: 0.950 Hom.: 14435

Bravo AF: 0.915

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jun 13, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified Benign:1

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PreventionGenetics, part of Exact Sciences

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	-0.94
CADD	Benign	0.36
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs1227042; hg19: chr10-73439101;