rs5969896

chrX-152430247-G-AchrX-152430247-G-C

Variant summary

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

The NM_000808.4(GABRA3):c.-27+20899C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 111,114 control chromosomes in the GnomAD database, including 1,334 homozygotes. There are 5,793 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 0.18 (1334 hom., 5793 hem., cov: 23)
• Consequence: GABRA3 NM_000808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRA3	NM_000808.4	c.-27+20899C>T		intron_variant		ENST00000370314.9
GABRA3	XM_006724811.4	c.-27+20899C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRA3	ENST00000370314.9	c.-27+20899C>T		intron_variant		1	NM_000808.4	P1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 19741 AN: 111059 Hom.: 1336 Cov.: 23 AF XY: 0.173 AC XY: 5765 AN XY: 33347

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0902

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.178 AC: 19759 AN: 111114 Hom.: 1334 Cov.: 23 AF XY: 0.173 AC XY: 5793 AN XY: 33412

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.186

Alfa AF: 0.168 Hom.: 10888

Bravo AF: 0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.36
Dann	Benign	0.30

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: rs5969896; hg19: chrX-151598719;