4-46992955-GAA-GAAAA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_000809.4(GABRA4):c.87-11_87-10dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.014 ( 25 hom., cov: 0)
Exomes 𝑓: 0.029 ( 26 hom. )
Consequence
GABRA4
NM_000809.4 intron
NM_000809.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0260
Genes affected
GABRA4 (HGNC:4078): (gamma-aminobutyric acid type A receptor subunit alpha4) Gamma-aminobutyric acid (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. This gene encodes subunit alpha-4, which is involved in the etiology of autism and eventually increases autism risk through interaction with another subunit, gamma-aminobutyric acid receptor beta-1 (GABRB1). Alternatively spliced transcript variants encoding different isoforms have been found in this gene.[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0142 (2053/144080) while in subpopulation EAS AF= 0.0405 (198/4890). AF 95% confidence interval is 0.0359. There are 25 homozygotes in gnomad4. There are 978 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2053 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABRA4 | NM_000809.4 | c.87-11_87-10dupTT | intron_variant | ENST00000264318.4 | NP_000800.2 | |||
GABRA4 | NM_001204266.2 | c.30-11_30-10dupTT | intron_variant | NP_001191195.1 | ||||
GABRA4 | NM_001204267.2 | c.30-11_30-10dupTT | intron_variant | NP_001191196.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GABRA4 | ENST00000264318.4 | c.87-10_87-9insTT | intron_variant | 1 | NM_000809.4 | ENSP00000264318.3 |
Frequencies
GnomAD3 genomes AF: 0.0142 AC: 2043AN: 144024Hom.: 24 Cov.: 0
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GnomAD4 exome AF: 0.0290 AC: 32859AN: 1133516Hom.: 26 Cov.: 19 AF XY: 0.0283 AC XY: 16241AN XY: 573028
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GnomAD4 genome AF: 0.0142 AC: 2053AN: 144080Hom.: 25 Cov.: 0 AF XY: 0.0140 AC XY: 978AN XY: 69690
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at