rs145868749
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_022124.6(CDH23):c.6275C>T(p.Thr2092Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,612,800 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_022124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.6275C>T | p.Thr2092Ile | missense_variant | 48/70 | ENST00000224721.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.6275C>T | p.Thr2092Ile | missense_variant | 48/70 | 5 | NM_022124.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00101 AC: 153AN: 152158Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000271 AC: 67AN: 247546Hom.: 0 AF XY: 0.000231 AC XY: 31AN XY: 134470
GnomAD4 exome AF: 0.000140 AC: 204AN: 1460524Hom.: 1 Cov.: 31 AF XY: 0.000120 AC XY: 87AN XY: 726380
GnomAD4 genome ? AF: 0.00102 AC: 155AN: 152276Hom.: 0 Cov.: 31 AF XY: 0.00114 AC XY: 85AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Thr2092Ile in Exon 48 of CDH23: This variant is not expected to have clinical si gnificance because it has been identified in 0.3% (10/3322) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs145868749). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at