10-71815240-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_022124.6(CDH23):c.10027G>A(p.Val3343Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000138 in 1,590,860 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 Uncertain significance (★).
Frequency
Consequence
NM_022124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000339 AC: 8AN: 235706Hom.: 0 AF XY: 0.0000389 AC XY: 5AN XY: 128428
GnomAD4 exome AF: 0.0000146 AC: 21AN: 1438592Hom.: 0 Cov.: 31 AF XY: 0.0000183 AC XY: 13AN XY: 711436
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74398
ClinVar
Submissions by phenotype
Usher syndrome type 1 Uncertain:1
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not provided Uncertain:1
The p.Val3343Met variant in CDH23 has been reported in 2 individuals with hearing loss who did not carry a second variant in the CDH23 gene (Mizutari 2015, LMM unpublished data). It has also been identified in 0.02% (4/17756) of East Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis do not provide strong support for or against an impact to the protein. In summary, the clinical significance of the p.Val3343Met variant is uncertain. ACMG/AMP Criteria applied: PM2_Supporting. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at