10-71706971-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_022124.6(CDH23):c.3028C>T(p.Arg1010Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,607,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1010H) has been classified as Uncertain significance.
Frequency
Consequence
NM_022124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.3028C>T | p.Arg1010Cys | missense_variant | 26/70 | ENST00000224721.12 | |
CDH23 | NM_001171930.2 | c.3028C>T | p.Arg1010Cys | missense_variant | 26/32 | ||
CDH23 | NM_001171931.2 | c.3028C>T | p.Arg1010Cys | missense_variant | 26/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.3028C>T | p.Arg1010Cys | missense_variant | 26/70 | 5 | NM_022124.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000849 AC: 2AN: 235552Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 127900
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1454952Hom.: 0 Cov.: 31 AF XY: 0.0000166 AC XY: 12AN XY: 723016
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.3028C>T (p.R1010C) alteration is located in exon 26 (coding exon 25) of the CDH23 gene. This alteration results from a C to T substitution at nucleotide position 3028, causing the arginine (R) at amino acid position 1010 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at