rs1838467

chr5-161639156-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRA6	ENST00000518888.1	n.218-1138G>A		intron_variant, non_coding_transcript_variant		4
GABRA6	ENST00000522269.5	n.277-1138G>A		intron_variant, non_coding_transcript_variant		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;