rs279869

Positions:

• chr4-46305978-G-T

Variant summary

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

The NM_000807.4(GABRA2):​c.560-267C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,882 control chromosomes in the GnomAD database, including 20,493 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 0.50 (20493 hom., cov: 31)
• Consequence: GABRA2 NM_000807.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABRA2	NM_000807.4	c.560-267C>A		intron_variant		ENST00000381620.9	NP_000798.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRA2	ENST00000381620.9	c.560-267C>A		intron_variant		1	NM_000807.4	ENSP00000371033.4

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76409 AN: 151764 Hom.: 20442 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.504 AC: 76519 AN: 151882 Hom.: 20493 Cov.: 31 AF XY: 0.500 AC XY: 37111 AN XY: 74220

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.458

Alfa AF: 0.482 Hom.: 2284

Bravo AF: 0.524

Asia WGS AF: 0.404 AC: 1403 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.26

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: rs279869; hg19: chr4-46307995;