10-71397276-CCGAGG-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_022124.6(CDH23):c.-35_-31delAGGCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 172,870 control chromosomes in the GnomAD database, including 1,393 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_022124.6 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.109 AC: 16378AN: 150180Hom.: 1304 Cov.: 0
GnomAD3 exomes AF: 0.0528 AC: 13AN: 246Hom.: 0 AF XY: 0.0493 AC XY: 7AN XY: 142
GnomAD4 exome AF: 0.0675 AC: 1524AN: 22584Hom.: 80 AF XY: 0.0692 AC XY: 986AN XY: 14252
GnomAD4 genome AF: 0.109 AC: 16417AN: 150286Hom.: 1313 Cov.: 0 AF XY: 0.109 AC XY: 7987AN XY: 73344
ClinVar
Submissions by phenotype
not specified Benign:2
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Outside ROI, common in our data set -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
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Hearing loss, autosomal recessive Benign:1
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Retinitis pigmentosa-deafness syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at