rs1440130

chr4-46331236-T-C

Variant summary

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

The NM_000807.4(GABRA2):c.255+1379A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,016 control chromosomes in the GnomAD database, including 13,423 homozygotes. 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 0.41 (13423 hom., cov: 32)
• Consequence: GABRA2 NM_000807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

Genes affected

GABRA2 (HGNC:4076): (gamma-aminobutyric acid type A receptor subunit alpha2) 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRA2	NM_000807.4	c.255+1379A>G		intron_variant		ENST00000381620.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRA2	ENST00000381620.9	c.255+1379A>G		intron_variant		1	NM_000807.4	P2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62764 AN: 151898 Hom.: 13405 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.413 AC: 62815 AN: 152016 Hom.: 13423 Cov.: 32 AF XY: 0.416 AC XY: 30901 AN XY: 74288

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.393

Alfa AF: 0.441 Hom.: 3048

Bravo AF: 0.413

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.0
Dann	Benign	0.49

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: rs1440130; hg19: chr4-46333253;