chr10-71724072-G-A
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBS1_Supporting
The NM_022124.6(CDH23):c.3397G>A(p.Glu1133Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000596 in 1,560,284 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. E1133E) has been classified as Likely benign.
Frequency
Consequence
NM_022124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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CDH23 | NM_022124.6 | c.3397G>A | p.Glu1133Lys | missense_variant | Exon 29 of 70 | ENST00000224721.12 | NP_071407.4 | |
CDH23 | NM_001171930.2 | c.3397G>A | p.Glu1133Lys | missense_variant | Exon 29 of 32 | NP_001165401.1 | ||
C10orf105 | NM_001168390.2 | c.-5-7730C>T | intron_variant | Intron 1 of 1 | NP_001161862.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152188Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000215 AC: 36AN: 167448 AF XY: 0.000169 show subpopulations
GnomAD4 exome AF: 0.0000575 AC: 81AN: 1408096Hom.: 0 Cov.: 32 AF XY: 0.0000503 AC XY: 35AN XY: 695254 show subpopulations
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74346 show subpopulations
ClinVar
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 12;C1832845:Usher syndrome type 1D;C4539685:Pituitary adenoma 5, multiple types Uncertain:1
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not specified Uncertain:1
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Pituitary adenoma 5, multiple types Uncertain:1
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Usher syndrome type 1 Uncertain:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at