rs768735888
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_019098.5(CNGB3):c.1516del(p.Val506SerfsTer3) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000031 in 1,613,808 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
CNGB3
NM_019098.5 frameshift
NM_019098.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.86
Genes affected
CNGB3 (HGNC:2153): (cyclic nucleotide gated channel subunit beta 3) This gene encodes the beta subunit of a cyclic nucleotide-gated ion channel. The encoded beta subunit appears to play a role in modulation of channel function in cone photoreceptors. This heterotetrameric channel is necessary for sensory transduction, and mutations in this gene have been associated with achromatopsia 3, progressive cone dystrophy, and juvenile macular degeneration, also known as Stargardt Disease. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 8-86626044-AC-A is Pathogenic according to our data. Variant chr8-86626044-AC-A is described in ClinVar as [Pathogenic]. Clinvar id is 427663.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-86626044-AC-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNGB3 | NM_019098.5 | c.1516del | p.Val506SerfsTer3 | frameshift_variant | 13/18 | ENST00000320005.6 | |
CNGB3 | XM_011517138.3 | c.1102del | p.Val368SerfsTer3 | frameshift_variant | 11/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNGB3 | ENST00000320005.6 | c.1516del | p.Val506SerfsTer3 | frameshift_variant | 13/18 | 1 | NM_019098.5 | P1 | |
CNGB3 | ENST00000681546.1 | n.1336del | non_coding_transcript_exon_variant | 8/13 | |||||
CNGB3 | ENST00000681746.1 | c.1516del | p.Val506SerfsTer3 | frameshift_variant, NMD_transcript_variant | 13/19 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250994Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135632
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461530Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727064
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74466
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Achromatopsia 3 Pathogenic:1
Pathogenic, no assertion criteria provided | research | Molecular Genetics Laboratory, Institute for Ophthalmic Research | Mar 27, 2017 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2023 | This sequence change creates a premature translational stop signal (p.Val506Serfs*3) in the CNGB3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CNGB3 are known to be pathogenic (PMID: 28795510). This variant is present in population databases (rs768735888, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with achromatopsia (PMID: 28795510). ClinVar contains an entry for this variant (Variation ID: 427663). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at