chr10-71809956-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS1
The NM_022124.6(CDH23):c.8859C>T(p.Asp2953Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000312 in 1,612,330 control chromosomes in the GnomAD database, including 1 homozygotes. 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 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.8859C>T | p.Asp2953Asp | synonymous_variant | Exon 61 of 70 | ENST00000224721.12 | NP_071407.4 | |
CDH23 | NM_001171933.1 | c.2139C>T | p.Asp713Asp | synonymous_variant | Exon 14 of 23 | NP_001165404.1 | ||
CDH23 | NM_001171934.1 | c.2139C>T | p.Asp713Asp | synonymous_variant | Exon 14 of 22 | NP_001165405.1 | ||
LOC124902446 | XR_007062185.1 | n.1937G>A | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000995 AC: 246AN: 247296Hom.: 0 AF XY: 0.00104 AC XY: 140AN XY: 134350
GnomAD4 exome AF: 0.000303 AC: 442AN: 1460024Hom.: 1 Cov.: 32 AF XY: 0.000296 AC XY: 215AN XY: 726326
GnomAD4 genome AF: 0.000401 AC: 61AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000537 AC XY: 40AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:3
This variant is associated with the following publications: (PMID: 17850630) -
CDH23: BP4, BP7, BS1 -
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Autosomal recessive nonsyndromic hearing loss 12 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not specified Benign:1
p.Asp2953Asp in exon 61 of CDH23: This variant is not expected to have clinical significance because has been identified in 1.3% (111/8568) of East Asian chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs11000008). -
Usher syndrome type 1D Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Usher syndrome type 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at