10-71566886-G-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_022124.6(CDH23):ā€‹c.574G>Cā€‹(p.Glu192Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000387 in 1,613,840 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: š‘“ 0.00031 ( 0 hom., cov: 33)
Exomes š‘“: 0.00039 ( 7 hom. )

Consequence

CDH23
NM_022124.6 missense

Scores

4
15

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:6

Conservation

PhyloP100: 2.06
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.015382856).
BP6
Variant 10-71566886-G-C is Benign according to our data. Variant chr10-71566886-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 178295.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=2, Likely_benign=2, Benign=2}. Variant chr10-71566886-G-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000309 (47/152252) while in subpopulation SAS AF= 0.00332 (16/4814). AF 95% confidence interval is 0.00208. There are 0 homozygotes in gnomad4. There are 28 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 7 AD,AR,Digenic gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDH23NM_022124.6 linkc.574G>C p.Glu192Gln missense_variant 7/70 ENST00000224721.12 NP_071407.4 Q9H251-1Q6P152

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDH23ENST00000224721.12 linkc.574G>C p.Glu192Gln missense_variant 7/705 NM_022124.6 ENSP00000224721.9 Q9H251-1

Frequencies

GnomAD3 genomes
AF:
0.000309
AC:
47
AN:
152134
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00433
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00332
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000687
AC:
171
AN:
249006
Hom.:
3
AF XY:
0.000873
AC XY:
118
AN XY:
135120
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00397
Gnomad EAS exome
AF:
0.0000556
Gnomad SAS exome
AF:
0.00281
Gnomad FIN exome
AF:
0.0000466
Gnomad NFE exome
AF:
0.000345
Gnomad OTH exome
AF:
0.000661
GnomAD4 exome
AF:
0.000395
AC:
577
AN:
1461588
Hom.:
7
Cov.:
31
AF XY:
0.000465
AC XY:
338
AN XY:
727086
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00337
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00277
Gnomad4 FIN exome
AF:
0.000206
Gnomad4 NFE exome
AF:
0.000169
Gnomad4 OTH exome
AF:
0.000712
GnomAD4 genome
AF:
0.000309
AC:
47
AN:
152252
Hom.:
0
Cov.:
33
AF XY:
0.000376
AC XY:
28
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00433
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00332
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000410
Hom.:
0
Bravo
AF:
0.000185
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000239
AC:
2
ExAC
AF:
0.000802
AC:
97
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000178

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:6
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 30, 2024- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2024CDH23: BP4, BS2 -
Benign, criteria provided, single submitterclinical testingGeneDxNov 30, 2018This variant is associated with the following publications: (PMID: 24916380) -
Usher syndrome type 1D Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Autosomal recessive nonsyndromic hearing loss 12 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 20, 2017p.Glu192Gln in exon 7 of CDH23: This variant is not expected to have clinical si gnificance because it has been identified in 0.3% (48/16480) of South Asian chro mosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.or g; dbSNP rs199514829). -
CDH23-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesNov 01, 2022This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Usher syndrome type 1 Benign:1
Benign, no assertion criteria providedclinical testingNatera, Inc.Jan 30, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.072
BayesDel_addAF
Benign
-0.55
T
BayesDel_noAF
Benign
-0.56
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.015
T;T;T;.;.;.;T;.;.
Eigen
Benign
0.16
Eigen_PC
Uncertain
0.30
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.93
D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.015
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.49
T
MutationAssessor
Benign
0.26
.;.;N;N;.;.;.;.;.
PrimateAI
Benign
0.44
T
PROVEAN
Benign
-0.54
N;.;.;.;.;.;.;.;.
REVEL
Benign
0.083
Sift
Benign
0.24
T;.;.;.;.;.;.;.;.
Sift4G
Benign
0.27
T;T;.;T;T;T;T;.;.
Polyphen
0.54, 0.57
.;.;P;P;.;.;.;.;.
Vest4
0.51
MVP
0.69
ClinPred
0.024
T
GERP RS
5.7
Varity_R
0.17
gMVP
0.22

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.

Other links and lift over

dbSNP: rs199514829; hg19: chr10-73326643; API