chr10-71741696-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_022124.6(CDH23):c.4620C>A(p.Asn1540Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,606,014 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. N1540N) has been classified as Likely benign.
Frequency
Consequence
NM_022124.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.4620C>A | p.Asn1540Lys | missense_variant, splice_region_variant | 38/70 | ENST00000224721.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.4620C>A | p.Asn1540Lys | missense_variant, splice_region_variant | 38/70 | 5 | NM_022124.6 | P1 | |
CDH23 | ENST00000398792.3 | n.1309C>A | splice_region_variant, non_coding_transcript_exon_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000424 AC: 1AN: 235762Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128032
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1453798Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 722298
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at