rs1554604525
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The ENST00000320005.6(CNGB3):c.2359del(p.Ser787AlafsTer42) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. S787S) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
CNGB3
ENST00000320005.6 frameshift
ENST00000320005.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.31
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 Uncertain_significance. Variant got 5 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0292 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 8-86575874-CT-C is Pathogenic according to our data. Variant chr8-86575874-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 427668.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr8-86575874-CT-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNGB3 | NM_019098.5 | c.2359del | p.Ser787AlafsTer42 | frameshift_variant | 18/18 | ENST00000320005.6 | NP_061971.3 | |
CNGB3 | XM_011517138.3 | c.1945del | p.Ser649AlafsTer42 | frameshift_variant | 16/16 | XP_011515440.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNGB3 | ENST00000320005.6 | c.2359del | p.Ser787AlafsTer42 | frameshift_variant | 18/18 | 1 | NM_019098.5 | ENSP00000316605 | P1 | |
CNGB3 | ENST00000517327.5 | c.276+2814del | intron_variant | 3 | ENSP00000428329 | |||||
CNGB3 | ENST00000681546.1 | n.2179del | non_coding_transcript_exon_variant | 13/13 | ||||||
CNGB3 | ENST00000681746.1 | c.*770del | 3_prime_UTR_variant, NMD_transcript_variant | 19/19 | ENSP00000505959 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
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 | - - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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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