rs3811995

Positions:

• chr5-161685687-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000518888.1(GABRA6):​n.293-12C>T variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 508,884 control chromosomes in the GnomAD database, including 65,853 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 0.48 (18002 hom., cov: 31)
  • Exomes 𝑓: 0.51 (47851 hom.)
• Consequence: GABRA6 ENST00000518888.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

GABRA6 (HGNC:4080): (gamma-aminobutyric acid type A receptor subunit alpha6) 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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.12).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABRA6	NM_000811.3			upstream_gene_variant		ENST00000274545.10	NP_000802.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRA6	ENST00000518888.1	n.293-12C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		4
GABRA6	ENST00000522269.5	n.352-543C>T		intron_variant, non_coding_transcript_variant		4
GABRA6	ENST00000274545.10			upstream_gene_variant		1	NM_000811.3	ENSP00000274545	P1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72420 AN: 151854 Hom.: 18001 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.453

GnomAD4 exome AF: 0.509 AC: 181763 AN: 356912 Hom.: 47851 Cov.: 0 AF XY: 0.506 AC XY: 95840 AN XY: 189510

Gnomad4 AFR exome AF: 0.360

Gnomad4 AMR exome AF: 0.379

Gnomad4 ASJ exome AF: 0.524

Gnomad4 EAS exome AF: 0.308

Gnomad4 SAS exome AF: 0.425

Gnomad4 FIN exome AF: 0.535

Gnomad4 NFE exome AF: 0.563

Gnomad4 OTH exome AF: 0.501

GnomAD4 genome AF: 0.477 AC: 72429 AN: 151972 Hom.: 18002 Cov.: 31 AF XY: 0.474 AC XY: 35226 AN XY: 74284

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.449

Alfa AF: 0.540 Hom.: 21831

Bravo AF: 0.458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.12
CADD	Benign	19
DANN	Benign	0.94

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: rs3811995; hg19: chr5-161112693; COSMIC: COSV50878712; COSMIC: COSV50878712;