10-71510096-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_022124.6(CDH23):āc.160C>Gā(p.Gln54Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000211 in 1,613,916 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_022124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000923 AC: 23AN: 249294Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135246
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461696Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727134
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74362
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
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CDH23-related disorder Uncertain:1
The CDH23 c.160C>G variant is predicted to result in the amino acid substitution p.Gln54Glu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.064% of alleles in individuals of Latino descent in gnomAD, which my be too common to be an unreported cause of disease. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Inborn genetic diseases Uncertain:1
The c.160C>G (p.Q54E) alteration is located in exon 4 (coding exon 3) of the CDH23 gene. This alteration results from a C to G substitution at nucleotide position 160, causing the glutamine (Q) at amino acid position 54 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Usher syndrome type 1 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at