rs12372959
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_033223.5(GABRG3):c.270+65688C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,120 control chromosomes in the GnomAD database, including 4,240 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 0.23 ( 4240 hom., cov: 32)
Consequence
GABRG3
NM_033223.5 intron
NM_033223.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.90
Genes affected
GABRG3 (HGNC:4088): (gamma-aminobutyric acid type A receptor subunit gamma3) This gene encodes a gamma-aminobutyric acid (GABA) receptor. 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. GABA-A receptors are pentameric, consisting of proteins from several subunit classes: alpha, beta, gamma, delta and rho. The protein encoded by this gene is a gamma subunit, which contains the benzodiazepine binding site. Two transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Aug 2012]
GABRG3-AS1 (HGNC:40249): (GABRG3 antisense RNA 1)
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRG3 | NM_033223.5 | c.270+65688C>T | intron_variant | ENST00000615808.5 | |||
LOC107984766 | XR_001751460.2 | n.225-3829G>A | intron_variant, non_coding_transcript_variant | ||||
GABRG3 | NM_001270873.2 | c.270+65688C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRG3 | ENST00000615808.5 | c.270+65688C>T | intron_variant | 1 | NM_033223.5 | P1 | |||
GABRG3-AS1 | ENST00000660679.1 | n.376+8314G>A | intron_variant, non_coding_transcript_variant | ||||||
GABRG3 | ENST00000555083.5 | c.270+65688C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.230 AC: 34957AN: 152002Hom.: 4245 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.230 AC: 34955AN: 152120Hom.: 4240 Cov.: 32 AF XY: 0.227 AC XY: 16873AN XY: 74344
GnomAD4 genome
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74344
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399
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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