rs1838467

Variant names:

• chr5-161639156-G-A
• rs1838467
• ENST00000518888.1:n.218-1138G>A

Variant summary

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

The ENST00000518888.1(GABRA6):​n.218-1138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,098 control chromosomes in the GnomAD database, including 2,228 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 0.15 (2228 hom., cov: 32)
• Consequence: GABRA6 ENST00000518888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRA6	ENST00000518888.1	n.218-1138G>A		intron_variant	Intron 2 of 3	4
GABRA6	ENST00000522269.5	n.277-1138G>A		intron_variant	Intron 3 of 6	4

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22232 AN: 151980 Hom.: 2223 Cov.: 32

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.146 AC: 22255 AN: 152098 Hom.: 2228 Cov.: 32 AF XY: 0.150 AC XY: 11159 AN XY: 74358

Gnomad4 AFR AF: 0.0369

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.0926

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.161

Alfa AF: 0.155 Hom.: 1068

Bravo AF: 0.151

Asia WGS AF: 0.155 AC: 540 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	3.5
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1838467; hg19: chr5-161066162;