chr10-71810548-ACCG-A
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM4_SupportingPP5_Strong
The NM_022124.6(CDH23):c.9058_9060delCGC(p.Arg3020del) variant causes a conservative inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_022124.6 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.9058_9060delCGC | p.Arg3020del | conservative_inframe_deletion | Exon 62 of 70 | ENST00000224721.12 | NP_071407.4 | |
CDH23 | NM_001171933.1 | c.2338_2340delCGC | p.Arg780del | conservative_inframe_deletion | Exon 15 of 23 | NP_001165404.1 | ||
CDH23 | NM_001171934.1 | c.2338_2340delCGC | p.Arg780del | conservative_inframe_deletion | Exon 15 of 22 | NP_001165405.1 | ||
LOC124902446 | XR_007062185.1 | n.1342_1344delCGG | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:1
- -
This variant, c.9058_9060del, results in the deletion of 1 amino acid(s) of the CDH23 protein (p.Arg3020del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CDH23-related conditions. ClinVar contains an entry for this variant (Variation ID: 191267). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Usher syndrome type 1D Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at