chr10-71785622-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_022124.6(CDH23):c.5713-9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000218 in 1,562,032 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 27AN: 206210Hom.: 0 AF XY: 0.0000814 AC XY: 9AN XY: 110574
GnomAD4 exome AF: 0.0000199 AC: 28AN: 1409702Hom.: 0 Cov.: 28 AF XY: 0.0000157 AC XY: 11AN XY: 699846
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant classified as Uncertain Significance - Favor Benign. The 5713-9A>G varia nt in CDH23 has not been reported in the literature nor previously identified by our laboratory. This variant is located in the 3' splice region. Although posit ion -9 is part of the splice site region, the reference sequence was already div ergent from consensus (normally a T or C at this position) and therefore computa tional tools do not predict further divergence of the splice site from the conse nsus sequence. This would suggest an unlikely impact to splicing; however, the p redictability of these tools to assess splicing impact is unknown and therefore we cannot rule out an effect. In summary, the clinical significance of this vari ant cannot be determined with certainty; however, we would lean towards a more l ikely benign role. -
CDH23-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at