X-152378770-C-T

Position:

• chrX-152378770-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000808.4(GABRA3):​c.-26-14174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 109,989 control chromosomes in the GnomAD database, including 5,308 homozygotes. There are 11,602 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 0.36 (5308 hom., 11602 hem., cov: 23)
• Consequence: GABRA3 NM_000808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABRA3	NM_000808.4	c.-26-14174G>A		intron_variant		ENST00000370314.9	NP_000799.1
GABRA3	XM_006724811.4	c.-26-14174G>A		intron_variant			XP_006724874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRA3	ENST00000370314.9	c.-26-14174G>A		intron_variant		1	NM_000808.4	ENSP00000359337.4
GABRA3	ENST00000535043.1	c.-27+10536G>A		intron_variant		1		ENSP00000443527.1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 39937 AN: 109937 Hom.: 5301 Cov.: 23 AF XY: 0.358 AC XY: 11588 AN XY: 32343

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.432

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.363 AC: 39952 AN: 109989 Hom.: 5308 Cov.: 23 AF XY: 0.358 AC XY: 11602 AN XY: 32405

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.367

Alfa AF: 0.359 Hom.: 2685

Bravo AF: 0.370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs4828694; hg19: chrX-151547242;