dbSNP rs3811995: GABRA6:n.293-12C>T (chr5-161685687-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4BA1

The ENST00000518888.1(GABRA6):n.293-12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 508,884 control chromosomes in the GnomAD database, including 65,853 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 0.48 ( 18002 hom., cov: 31)

Exomes 𝑓: 0.51 ( 47851 hom. )

Consequence

GABRA6
ENST00000518888.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.09

Publications

9 publications found

Variant links:

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]

GABRA6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.12).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518888.1. 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.-303C>T		upstream_gene	N/A	NP_000802.2	Q16445

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GABRA6	ENST00000518888.1	TSL:4	n.293-12C>T	intron	N/A
GABRA6	ENST00000522269.5	TSL:4	n.352-543C>T	intron	N/A
GABRA6	ENST00000274545.10	TSL:1 MANE Select	c.-303C>T	upstream_gene	N/A	ENSP00000274545.5	Q16445

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72420

AN:

151854

Hom.:

18001

Cov.:

show subpopulations

Gnomad AFR

AF:

0.357

Gnomad AMI

AF:

0.428

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.526

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.552

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.566

Gnomad OTH

AF:

0.453

GnomAD4 exome

AF:

0.509

AC:

181763

AN:

356912

Hom.:

47851

Cov.:

AF XY:

0.506

AC XY:

95840

AN XY:

189510

show subpopulations

African (AFR)

AF:

0.360

AC:

3788

AN:

10522

American (AMR)

AF:

0.379

AC:

6092

AN:

16076

Ashkenazi Jewish (ASJ)

AF:

0.524

AC:

5577

AN:

10648

East Asian (EAS)

AF:

0.308

AC:

7090

AN:

23044

South Asian (SAS)

AF:

0.425

AC:

17684

AN:

41650

European-Finnish (FIN)

AF:

0.535

AC:

10768

AN:

20116

Middle Eastern (MID)

AF:

0.481

AC:

751

AN:

1562

European-Non Finnish (NFE)

AF:

0.563

AC:

119713

AN:

212750

Other (OTH)

AF:

0.501

AC:

10300

AN:

20544

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

3779

7558

11336

15115

18894

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

526

1052

1578

2104

2630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.477

AC:

72429

AN:

151972

Hom.:

18002

Cov.:

AF XY:

0.474

AC XY:

35226

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.356

AC:

14774

AN:

41448

American (AMR)

AF:

0.425

AC:

6492

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.526

AC:

1828

AN:

3472

East Asian (EAS)

AF:

0.306

AC:

1582

AN:

5172

South Asian (SAS)

AF:

0.413

AC:

1989

AN:

4816

European-Finnish (FIN)

AF:

0.552

AC:

5823

AN:

10558

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.566

AC:

38464

AN:

67928

Other (OTH)

AF:

0.449

AC:

947

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1920

3840

5760

7680

9600

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.528

Hom.:

27508

Bravo

AF:

0.458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.12

CADD

Benign

(source)

DANN

Benign

0.94

PhyloP100

1.1

PromoterAI

-0.032

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over