5-161695842-G-C

Variant names:

• chr5-161695842-G-C
• rs6883829
• NM_000811.3:c.1086+3642G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000811.3(GABRA6):​c.1086+3642G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,302 control chromosomes in the GnomAD database, including 24,677 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 0.56 (24677 hom., cov: 30)
• Consequence: GABRA6 NM_000811.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000811.3. 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
	GABRA6	NM_000811.3	MANE Select	c.1086+3642G>C		intron	N/A	NP_000802.2	Q16445

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRA6	ENST00000274545.10	TSL:1 MANE Select	c.1086+3642G>C		intron	N/A	ENSP00000274545.5	Q16445
	GABRA6	ENST00000523217.5	TSL:5	c.1056+3642G>C		intron	N/A	ENSP00000430527.1	E7EV53
	GABRA6	ENST00000521520.1	TSL:2	n.1079+3642G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85399 AN: 151188 Hom.: 24675 Cov.: 30

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.565 AC: 85419 AN: 151302 Hom.: 24677 Cov.: 30 AF XY: 0.561 AC XY: 41433 AN XY: 73888

African (AFR) AF: 0.483 AC: 19877 AN: 41140

American (AMR) AF: 0.509 AC: 7734 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2188 AN: 3464

East Asian (EAS) AF: 0.308 AC: 1574 AN: 5112

South Asian (SAS) AF: 0.484 AC: 2314 AN: 4780

European-Finnish (FIN) AF: 0.611 AC: 6397 AN: 10464

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43508 AN: 67860

Other (OTH) AF: 0.560 AC: 1179 AN: 2104

Alfa AF: 0.595 Hom.: 3263

Bravo AF: 0.549

Asia WGS AF: 0.376 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.32
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6883829; hg19: chr5-161122848; COSMIC: COSV50878784;