10-71806223-CG-TT
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 3P and 8B. PM2PP3BP6_Very_Strong
The NM_022124.6(CDH23):c.8120_8121delCGinsTT(p.Pro2707Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in Lovd. Synonymous variant affecting the same amino acid position (i.e. P2707P) has been classified as Benign.
Frequency
Consequence
NM_022124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.8120_8121delCGinsTT | p.Pro2707Leu | missense_variant | ENST00000224721.12 | NP_071407.4 | ||
CDH23 | NM_001171933.1 | c.1400_1401delCGinsTT | p.Pro467Leu | missense_variant | NP_001165404.1 | |||
CDH23 | NM_001171934.1 | c.1400_1401delCGinsTT | p.Pro467Leu | missense_variant | NP_001165405.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Benign:2
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c.8120_8121delinsTT (p.Pro2707Leu) in exon 57 of CDH23: This variant is not exp ected to have clinical significance because it has been identified in 1% (86/832 4) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http:// exac.broadinstitute.org; dbSNP rs377535432 and rs373230009). -
not provided Benign:2
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Autosomal recessive nonsyndromic hearing loss 12;C1832845:Usher syndrome type 1D;C4539685:Pituitary adenoma 5, multiple types Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at