rs1554619292
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_019098.5(CNGB3):c.190del(p.Glu64SerfsTer19) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,460,582 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. E64E) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_019098.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNGB3 | NM_019098.5 | c.190del | p.Glu64SerfsTer19 | frameshift_variant | 2/18 | ENST00000320005.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNGB3 | ENST00000320005.6 | c.190del | p.Glu64SerfsTer19 | frameshift_variant | 2/18 | 1 | NM_019098.5 | P1 | |
ENST00000519041.1 | n.449-21160del | intron_variant, non_coding_transcript_variant | 3 | ||||||
CNGB3 | ENST00000519777.1 | n.172del | non_coding_transcript_exon_variant | 2/4 | 2 | ||||
CNGB3 | ENST00000681746.1 | c.190del | p.Glu64SerfsTer19 | frameshift_variant, NMD_transcript_variant | 2/19 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460582Hom.: 0 Cov.: 39 AF XY: 0.00000275 AC XY: 2AN XY: 726662
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Achromatopsia 3 Pathogenic:2
Pathogenic, no assertion criteria provided | research | Molecular Genetics Laboratory, Institute for Ophthalmic Research | Mar 27, 2017 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Genomics England Pilot Project, Genomics England | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at