chr10-71712672-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_022124.6(CDH23):c.3228C>A(p.Gly1076=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,456 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. G1076G) 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.3228C>A | p.Gly1076= | synonymous_variant | 28/70 | ENST00000224721.12 | |
C10orf105 | NM_001164375.3 | c.*3264G>T | 3_prime_UTR_variant | 2/2 | ENST00000441508.4 | ||
CDH23 | NM_001171930.2 | c.3228C>A | p.Gly1076= | synonymous_variant | 28/32 | ||
C10orf105 | NM_001168390.2 | c.*3264G>T | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.3228C>A | p.Gly1076= | synonymous_variant | 28/70 | 5 | NM_022124.6 | P1 | |
C10orf105 | ENST00000441508.4 | c.*3264G>T | 3_prime_UTR_variant | 2/2 | 1 | NM_001164375.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248490Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135026
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461208Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726886
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at