10-71741696-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6BP7
The NM_022124.6(CDH23):c.4620C>T(p.Asn1540=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000666 in 1,606,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_022124.6 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.4620C>T | p.Asn1540= | splice_region_variant, synonymous_variant | 38/70 | ENST00000224721.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.4620C>T | p.Asn1540= | splice_region_variant, synonymous_variant | 38/70 | 5 | NM_022124.6 | P1 | |
CDH23 | ENST00000398792.3 | n.1309C>T | splice_region_variant, non_coding_transcript_exon_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000212 AC: 5AN: 235762Hom.: 0 AF XY: 0.0000234 AC XY: 3AN XY: 128032
GnomAD4 exome AF: 0.0000660 AC: 96AN: 1453798Hom.: 0 Cov.: 31 AF XY: 0.0000803 AC XY: 58AN XY: 722298
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74360
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 28, 2014 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 07, 2009 | - - |
Usher syndrome type 1 Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at