rs750841

Variant names:

• chrX-152297246-T-A
• rs750841
• NM_000808.4:c.263-12511A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000808.4(GABRA3):​c.263-12511A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 110,736 control chromosomes in the GnomAD database, including 2,673 homozygotes. There are 6,991 hemizygotes in GnomAD. 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 0.22 (2673 hom., 6991 hem., cov: 22)
• Consequence: GABRA3 NM_000808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 3 publications found

Genes affected

GABRA3 (HGNC:4077): (gamma-aminobutyric acid type A receptor subunit alpha3) 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. [provided by RefSeq, Jul 2008]

GABRA3 Gene-Disease associations (from GenCC):

• epilepsy, X-linked 2, with or without impaired intellectual development and dysmorphic features

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Illumina

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000808.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRA3	NM_000808.4	MANE Select	c.263-12511A>T		intron	N/A	NP_000799.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRA3	ENST00000370314.9	TSL:1 MANE Select	c.263-12511A>T		intron	N/A	ENSP00000359337.4
	GABRA3	ENST00000535043.1	TSL:1	c.263-12511A>T		intron	N/A	ENSP00000443527.1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 24774 AN: 110681 Hom.: 2672 Cov.: 22

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.204

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.224 AC: 24816 AN: 110736 Hom.: 2673 Cov.: 22 AF XY: 0.212 AC XY: 6991 AN XY: 33004

African (AFR) AF: 0.428 AC: 12974 AN: 30288

American (AMR) AF: 0.115 AC: 1193 AN: 10401

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 440 AN: 2637

East Asian (EAS) AF: 0.197 AC: 692 AN: 3504

South Asian (SAS) AF: 0.177 AC: 463 AN: 2612

European-Finnish (FIN) AF: 0.163 AC: 961 AN: 5895

Middle Eastern (MID) AF: 0.173 AC: 37 AN: 214

European-Non Finnish (NFE) AF: 0.145 AC: 7670 AN: 52981

Other (OTH) AF: 0.201 AC: 307 AN: 1524

Alfa AF: 0.196 Hom.: 1184

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.78
DANN	Benign	0.34
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs750841; hg19: chrX-151465718;