rs397515384
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001377295.2(GNAT2):c.461+24G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
GNAT2
NM_001377295.2 intron
NM_001377295.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.53
Genes affected
GNAT2 (HGNC:4394): (G protein subunit alpha transducin 2) Transducin is a 3-subunit guanine nucleotide-binding protein (G protein) which stimulates the coupling of rhodopsin and cGMP-phoshodiesterase during visual impulses. The transducin alpha subunits in rods and cones are encoded by separate genes. This gene encodes the alpha subunit in cones. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAT2 | NM_001377295.2 | c.461+24G>A | intron_variant | ENST00000679935.1 | |||
GNAT2 | NM_001379232.1 | c.461+24G>A | intron_variant | ||||
GNAT2 | NM_005272.5 | c.461+24G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAT2 | ENST00000679935.1 | c.461+24G>A | intron_variant | NM_001377295.2 | P1 | ||||
GNAT2 | ENST00000351050.8 | c.461+24G>A | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 28
GnomAD4 exome
Cov.:
28
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Achromatopsia 4 Pathogenic:1Uncertain:1Other:1
Uncertain significance, no assertion criteria provided | research | Molecular Genetics Laboratory, Institute for Ophthalmic Research | Jun 12, 2018 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 2002 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 3
DS_DL_spliceai
Position offset: 24
Find out detailed SpliceAI scores and Pangolin per-transcript scores at