rs1838467

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518888.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRA6	ENST00000518888.1	TSL:4	n.218-1138G>A		intron	N/A
	GABRA6	ENST00000522269.5	TSL:4	n.277-1138G>A		intron	N/A

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

African (AFR) AF: 0.0369 AC: 1533 AN: 41552

American (AMR) AF: 0.271 AC: 4134 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3464

East Asian (EAS) AF: 0.265 AC: 1368 AN: 5166

South Asian (SAS) AF: 0.0926 AC: 447 AN: 4828

European-Finnish (FIN) AF: 0.230 AC: 2436 AN: 10584

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11029 AN: 67926

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.155 Hom.: 1170

Bravo AF: 0.151

Asia WGS AF: 0.155 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.69
PhyloP100		-0.0020

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1838467;

hg19: chr5-161066162;