rs483353053
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_022124.6(CDH23):c.9510+19_9510+25del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00372 in 1,613,816 control chromosomes in the GnomAD database, including 178 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.020 ( 93 hom., cov: 33)
Exomes 𝑓: 0.0021 ( 85 hom. )
Consequence
CDH23
NM_022124.6 intron
NM_022124.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0120
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
Variant 10-71812624-GTCAGGCA-G is Benign according to our data. Variant chr10-71812624-GTCAGGCA-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 133306.We mark this variant Likely_benign, oryginal submissions are: {Benign=6, Uncertain_significance=1}. Variant chr10-71812624-GTCAGGCA-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0654 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.9510+19_9510+25del | intron_variant | ENST00000224721.12 | |||
LOC124902446 | XR_007062185.1 | n.128_134del | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.9510+19_9510+25del | intron_variant | 5 | NM_022124.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0197 AC: 2994AN: 152242Hom.: 93 Cov.: 33
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GnomAD3 exomes AF: 0.00507 AC: 1261AN: 248640Hom.: 30 AF XY: 0.00403 AC XY: 544AN XY: 135022
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GnomAD4 exome AF: 0.00206 AC: 3014AN: 1461456Hom.: 85 AF XY: 0.00183 AC XY: 1327AN XY: 727036
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GnomAD4 genome AF: 0.0197 AC: 2995AN: 152360Hom.: 93 Cov.: 33 AF XY: 0.0193 AC XY: 1440AN XY: 74514
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:7
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Usher syndrome type 1D Uncertain:1
Uncertain significance, criteria provided, single submitter | literature only | Molecular Genetics Laboratory; Baylor College of Medicine | - | - - |
Atypical Gaucher Disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 16, 2017 | 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. - |
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 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Metachromatic leukodystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at