Variant rs34826485 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_000811.3(GABRA6):c.639A>G(p.Gln213Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00766 in 1,613,366 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 9 hom., cov: 32)

Exomes 𝑓: 0.0079 ( 146 hom. )

Consequence

GABRA6
NM_000811.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.75

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:

GABRA6 (HGNC:):

GABRA6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 5-161689745-A-G is Benign according to our data. Variant chr5-161689745-A-G is described in ClinVar as [Benign]. Clinvar id is 477867.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.75 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00544 (829/152348) while in subpopulation SAS AF= 0.0381 (184/4830). AF 95% confidence interval is 0.0336. There are 9 homozygotes in gnomad4. There are 408 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABRA6	NM_000811.3 linkuse as main transcript	c.639A>G	p.Gln213Gln	synonymous_variant	6/9	ENST00000274545.10	NP_000802.2	Q16445

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRA6	ENST00000274545.10 linkuse as main transcript	c.639A>G	p.Gln213Gln	synonymous_variant	6/9	1	NM_000811.3	ENSP00000274545.5		Q16445

Frequencies

GnomAD3 genomes

AF:

0.00545

AC:

829

AN:

152230

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00432

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0377

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00657

Gnomad OTH

AF:

0.00861

GnomAD3 exomes

AF:

0.00934

AC:

2347

AN:

251216

Hom.:

AF XY:

0.0116

AC XY:

1570

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00416

Gnomad ASJ exome

AF:

0.0126

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0406

Gnomad FIN exome

AF:

0.00153

Gnomad NFE exome

AF:

0.00635

Gnomad OTH exome

AF:

0.00965

GnomAD4 exome

AF:

0.00789

AC:

11524

AN:

1461018

Hom.:

146

Cov.:

AF XY:

0.00914

AC XY:

6644

AN XY:

726878

show subpopulations

Gnomad4 AFR exome

AF:

0.00117

Gnomad4 AMR exome

AF:

0.00467

Gnomad4 ASJ exome

AF:

0.0133

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0407

Gnomad4 FIN exome

AF:

0.00198

Gnomad4 NFE exome

AF:

0.00600

Gnomad4 OTH exome

AF:

0.00871

GnomAD4 genome

AF:

0.00544

AC:

829

AN:

152348

Hom.:

Cov.:

AF XY:

0.00548

AC XY:

408

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00103

Gnomad4 AMR

AF:

0.00431

Gnomad4 ASJ

AF:

0.0150

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0381

Gnomad4 FIN

AF:

0.00122

Gnomad4 NFE

AF:

0.00657

Gnomad4 OTH

AF:

0.00805

Alfa

AF:

0.00616

Hom.:

Bravo

AF:

0.00471

Asia WGS

AF:

0.0100

AC:

AN:

3478

EpiCase

AF:

0.00922

EpiControl

AF:

0.0109

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Childhood absence epilepsy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 26, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

6.3

DANN

Benign

0.75

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over