rs4398085
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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+69986C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 150,348 control chromosomes in the GnomAD database, including 5,300 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 0.26 ( 5300 hom., cov: 30)
Consequence
GABRG3
NM_033223.5 intron
NM_033223.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.497
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=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRG3 | NM_033223.5 | c.270+69986C>T | intron_variant | ENST00000615808.5 | |||
LOC107984766 | XR_001751460.2 | n.224+2009G>A | intron_variant, non_coding_transcript_variant | ||||
GABRG3 | NM_001270873.2 | c.270+69986C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRG3 | ENST00000615808.5 | c.270+69986C>T | intron_variant | 1 | NM_033223.5 | P1 | |||
GABRG3-AS1 | ENST00000660679.1 | n.376+4016G>A | intron_variant, non_coding_transcript_variant | ||||||
GABRG3 | ENST00000555083.5 | c.270+69986C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.261 AC: 39216AN: 150260Hom.: 5298 Cov.: 30
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.261 AC: 39240AN: 150348Hom.: 5300 Cov.: 30 AF XY: 0.257 AC XY: 18875AN XY: 73338
GnomAD4 genome
?
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18875
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73338
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414
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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