rs279828
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000807.4(GABRA2):c.188-111T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 591,170 control chromosomes in the GnomAD database, including 54,964 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.41 ( 13459 hom., cov: 31)
Exomes 𝑓: 0.43 ( 41505 hom. )
Consequence
GABRA2
NM_000807.4 intron
NM_000807.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.105
Genes affected
GABRA2 (HGNC:4076): (gamma-aminobutyric acid type A receptor subunit alpha2) GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA-A receptors, which are ligand-gated chloride channels. Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. At least 16 distinct subunits of GABA-A receptors have been identified. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRA2 | NM_000807.4 | c.188-111T>G | intron_variant | ENST00000381620.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRA2 | ENST00000381620.9 | c.188-111T>G | intron_variant | 1 | NM_000807.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.413 AC: 62717AN: 151814Hom.: 13440 Cov.: 31
GnomAD3 genomes
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GnomAD4 exome AF: 0.429 AC: 188405AN: 439238Hom.: 41505 AF XY: 0.422 AC XY: 98957AN XY: 234344
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GnomAD4 genome ? AF: 0.413 AC: 62758AN: 151932Hom.: 13459 Cov.: 31 AF XY: 0.416 AC XY: 30874AN XY: 74272
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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