ENST00000518888.1:n.217+1302A>T

Variant names:

• chr5-161638198-A-T
• rs10515831
• ENST00000518888.1:n.217+1302A>T

Variant summary

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

The ENST00000518888.1(GABRA6):​n.217+1302A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 151,916 control chromosomes in the GnomAD database, including 2,714 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 0.17 (2714 hom., cov: 32)
• Consequence: GABRA6 ENST00000518888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 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.217+1302A>T		intron_variant	Intron 2 of 3	4
GABRA6	ENST00000522269.5	n.276+1302A>T		intron_variant	Intron 3 of 6	4

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25629 AN: 151798 Hom.: 2709 Cov.: 32

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.0804

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.169 AC: 25647 AN: 151916 Hom.: 2714 Cov.: 32 AF XY: 0.172 AC XY: 12760 AN XY: 74246

Gnomad4 AFR AF: 0.0638

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.191

Alfa AF: 0.185 Hom.: 366

Bravo AF: 0.163

Asia WGS AF: 0.378 AC: 1313 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.86
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515831; hg19: chr5-161065204;