X-152443154-A-T

Variant names:

• chrX-152443154-A-T
• rs10482215
• NM_000808.4:c.-27+7992T>A

Variant summary

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

The NM_000808.4(GABRA3):​c.-27+7992T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 111,234 control chromosomes in the GnomAD database, including 1,478 homozygotes. There are 6,068 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 0.19 (1478 hom., 6068 hem., cov: 23)
• Consequence: GABRA3 NM_000808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRA3	NM_000808.4	c.-27+7992T>A		intron_variant	Intron 1 of 9	ENST00000370314.9	NP_000799.1
GABRA3	XM_006724811.4	c.-27+7992T>A		intron_variant	Intron 1 of 8		XP_006724874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRA3	ENST00000370314.9	c.-27+7992T>A		intron_variant	Intron 1 of 9	1	NM_000808.4	ENSP00000359337.4

Frequencies

GnomAD3 genomes AF: 0.188 AC: 20857 AN: 111188 Hom.: 1480 Cov.: 23 AF XY: 0.181 AC XY: 6044 AN XY: 33440

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0938

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.254

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.188 AC: 20871 AN: 111234 Hom.: 1478 Cov.: 23 AF XY: 0.181 AC XY: 6068 AN XY: 33496

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.192

Alfa AF: 0.177 Hom.: 1011

Bravo AF: 0.195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.21

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: rs10482215; hg19: chrX-151611626;