rs200324241
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6BP7
The NM_022124.6(CDH23):c.1446C>A(p.Val482=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,614,002 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V482V) has been classified as Likely benign.
Frequency
Consequence
NM_022124.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.1446C>A | p.Val482= | synonymous_variant | 14/70 | ENST00000224721.12 | |
CDH23 | NM_001171930.2 | c.1446C>A | p.Val482= | synonymous_variant | 14/32 | ||
CDH23 | NM_001171931.2 | c.1446C>A | p.Val482= | synonymous_variant | 14/26 | ||
CDH23 | NM_052836.4 | c.1446C>A | p.Val482= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.1446C>A | p.Val482= | synonymous_variant | 14/70 | 5 | NM_022124.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000480 AC: 73AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000124 AC: 31AN: 249222Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135220
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461708Hom.: 1 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727136
GnomAD4 genome ? AF: 0.000479 AC: 73AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74456
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 15, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 11, 2016 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 11, 2014 | Val482Val in Exon 14A of CDH23: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 2/4254 African Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs200324241). - |
Usher syndrome type 1 Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 24, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at