chr10-71712775-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022124.6(CDH23):c.3331G>T(p.Val1111Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,678 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1111I) has been classified as Likely benign.
Frequency
Consequence
NM_022124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.3331G>T | p.Val1111Phe | missense_variant | 28/70 | ENST00000224721.12 | |
C10orf105 | NM_001164375.3 | c.*3161C>A | 3_prime_UTR_variant | 2/2 | ENST00000441508.4 | ||
CDH23 | NM_001171930.2 | c.3331G>T | p.Val1111Phe | missense_variant | 28/32 | ||
C10orf105 | NM_001168390.2 | c.*3161C>A | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.3331G>T | p.Val1111Phe | missense_variant | 28/70 | 5 | NM_022124.6 | P1 | |
C10orf105 | ENST00000441508.4 | c.*3161C>A | 3_prime_UTR_variant | 2/2 | 1 | NM_001164375.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245702Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133756
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460678Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726528
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Vitreoretinopathy Uncertain:1
Uncertain significance, no assertion criteria provided | research | Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet | Apr 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at