chr5-161638198-A-T

Position:

• chr5-161638198-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRA6	ENST00000518888.1	n.217+1302A>T		intron_variant, non_coding_transcript_variant		4
GABRA6	ENST00000522269.5	n.276+1302A>T		intron_variant, non_coding_transcript_variant		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;