chr10-71798451-C-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_022124.6(CDH23):c.6927C>A(p.Ala2309=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,816 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 (★★). Synonymous variant affecting the same amino acid position (i.e. A2309A) has been classified as Likely benign.
Frequency
Consequence
NM_022124.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.6927C>A | p.Ala2309= | synonymous_variant | 50/70 | ENST00000224721.12 | |
CDH23 | NM_001171933.1 | c.207C>A | p.Ala69= | synonymous_variant | 3/23 | ||
CDH23 | NM_001171934.1 | c.207C>A | p.Ala69= | synonymous_variant | 3/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.6927C>A | p.Ala2309= | synonymous_variant | 50/70 | 5 | NM_022124.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 249170Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135198
GnomAD4 exome AF: 0.000113 AC: 165AN: 1461604Hom.: 0 Cov.: 32 AF XY: 0.0000976 AC XY: 71AN XY: 727092
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | CDH23: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at