rs11959228

Variant names:

• chr5-161700105-A-G
• rs11959228
• NM_000811.3:c.1087-1393A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-161700105-A-G
• chr5-161700105-A-T

Variant summary

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

The NM_000811.3(GABRA6):​c.1087-1393A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,170 control chromosomes in the GnomAD database, including 47,205 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 0.78 (47205 hom., cov: 33)
• Consequence: GABRA6 NM_000811.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.883 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRA6	NM_000811.3	MANE Select	c.1087-1393A>G		intron	N/A	NP_000802.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRA6	ENST00000274545.10	TSL:1 MANE Select	c.1087-1393A>G		intron	N/A	ENSP00000274545.5
	GABRA6	ENST00000523217.5	TSL:5	c.1057-1393A>G		intron	N/A	ENSP00000430527.1
	GABRA6	ENST00000521520.1	TSL:2	n.1080-1393A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119326 AN: 152052 Hom.: 47190 Cov.: 33

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.785 AC: 119395 AN: 152170 Hom.: 47205 Cov.: 33 AF XY: 0.782 AC XY: 58168 AN XY: 74422

African (AFR) AF: 0.752 AC: 31198 AN: 41490

American (AMR) AF: 0.698 AC: 10679 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2912 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3123 AN: 5170

South Asian (SAS) AF: 0.906 AC: 4372 AN: 4828

European-Finnish (FIN) AF: 0.757 AC: 8024 AN: 10596

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56664 AN: 68006

Other (OTH) AF: 0.785 AC: 1659 AN: 2114

Alfa AF: 0.805 Hom.: 6531

Bravo AF: 0.772

Asia WGS AF: 0.772 AC: 2684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.58
PhyloP100		0.15
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: rs11959228; hg19: chr5-161127111; COSMIC: COSV50878807;