2-98369983-AG-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001298.3(CNGA3):c.9delG(p.Ile4SerfsTer15) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,526 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_001298.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNGA3 | ENST00000272602.7 | c.9delG | p.Ile4SerfsTer15 | frameshift_variant | Exon 2 of 8 | 1 | NM_001298.3 | ENSP00000272602.2 | ||
CNGA3 | ENST00000436404.6 | c.9delG | p.Ile4SerfsTer15 | frameshift_variant | Exon 2 of 7 | 1 | ENSP00000410070.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250928Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135630
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461526Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727040
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
This sequence change creates a premature translational stop signal (p.Ile4Serfs*15) in the CNGA3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CNGA3 are known to be pathogenic (PMID: 14757870, 24903488, 25637600). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CNGA3-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at