chr10-71803088-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_022124.6(CDH23):c.7660+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,605,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00087 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000085 ( 0 hom. )
Consequence
CDH23
NM_022124.6 intron
NM_022124.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 10-71803088-C-T is Benign according to our data. Variant chr10-71803088-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 162944.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.7660+13C>T | intron_variant | ENST00000224721.12 | |||
CDH23 | NM_001171933.1 | c.940+13C>T | intron_variant | ||||
CDH23 | NM_001171934.1 | c.940+13C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.7660+13C>T | intron_variant | 5 | NM_022124.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000867 AC: 132AN: 152204Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000284 AC: 70AN: 246360Hom.: 0 AF XY: 0.000202 AC XY: 27AN XY: 133536
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GnomAD4 exome AF: 0.0000847 AC: 123AN: 1452678Hom.: 0 Cov.: 40 AF XY: 0.0000527 AC XY: 38AN XY: 720846
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GnomAD4 genome AF: 0.000867 AC: 132AN: 152322Hom.: 0 Cov.: 31 AF XY: 0.000846 AC XY: 63AN XY: 74492
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 24, 2021 | See Variant Classification Assertion Criteria. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 25, 2016 | 7660+13C>T in Intron 54 of CDH23: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus seq uence and has been identified in 0.4% (40/9782) of African chromosomes by the Ex ome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs374011 250). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at