Variant rs3750344 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_005458.8(GABBR2):c.360A>G(p.Ala120Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 1,613,340 control chromosomes in the GnomAD database, including 24,329 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 2733 hom., cov: 34)

Exomes 𝑓: 0.17 ( 21596 hom. )

Consequence

GABBR2
NM_005458.8 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.30

Variant links:

Genes affected

GABBR2 (HGNC:4507): (gamma-aminobutyric acid type B receptor subunit 2) The multi-pass membrane protein encoded by this gene belongs to the G-protein coupled receptor 3 family and GABA-B receptor subfamily. The GABA-B receptors inhibit neuronal activity through G protein-coupled second-messenger systems, which regulate the release of neurotransmitters, and the activity of ion channels and adenylyl cyclase. This receptor subunit forms an active heterodimeric complex with GABA-B receptor subunit 1, neither of which is effective on its own. Allelic variants of this gene have been associated with nicotine dependence.[provided by RefSeq, Jan 2010]

GABBR2 links:

GABBR2 (HGNC:):

GABBR2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 9-98578034-T-C is Benign according to our data. Variant chr9-98578034-T-C is described in ClinVar as [Benign]. Clinvar id is 132156.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.3 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABBR2	NM_005458.8 linkuse as main transcript	c.360A>G	p.Ala120Ala	synonymous_variant	2/19	ENST00000259455.4	NP_005449.5	O75899H9NIL8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GABBR2	ENST00000259455.4 linkuse as main transcript	c.360A>G	p.Ala120Ala	synonymous_variant	2/19	1	NM_005458.8	ENSP00000259455.2	O75899
GABBR2	ENST00000637717.1 linkuse as main transcript	c.-25A>G		5_prime_UTR_variant	2/3	5		ENSP00000490789.1	A0A1B0GW60
GABBR2	ENST00000634227.1 linkuse as main transcript	n.134A>G		non_coding_transcript_exon_variant	2/6	5
GABBR2	ENST00000637410.1 linkuse as main transcript	n.138A>G		non_coding_transcript_exon_variant	2/19	5

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28229

AN:

152140

Hom.:

2733

Cov.:

show subpopulations

Gnomad AFR

AF:

0.234

Gnomad AMI

AF:

0.307

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.174

Gnomad OTH

AF:

0.167

GnomAD3 exomes

AF:

0.162

AC:

40695

AN:

251194

Hom.:

3741

AF XY:

0.163

AC XY:

22115

AN XY:

135760

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.0784

Gnomad ASJ exome

AF:

0.221

Gnomad EAS exome

AF:

0.146

Gnomad SAS exome

AF:

0.121

Gnomad FIN exome

AF:

0.187

Gnomad NFE exome

AF:

0.180

Gnomad OTH exome

AF:

0.182

GnomAD4 exome

AF:

0.168

AC:

245476

AN:

1461082

Hom.:

21596

Cov.:

AF XY:

0.168

AC XY:

121914

AN XY:

726890

show subpopulations

Gnomad4 AFR exome

AF:

0.239

Gnomad4 AMR exome

AF:

0.0835

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.122

Gnomad4 FIN exome

AF:

0.188

Gnomad4 NFE exome

AF:

0.170

Gnomad4 OTH exome

AF:

0.166

GnomAD4 genome

AF:

0.185

AC:

28237

AN:

152258

Hom.:

2733

Cov.:

AF XY:

0.185

AC XY:

13743

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.234

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.224

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.114

Gnomad4 FIN

AF:

0.192

Gnomad4 NFE

AF:

0.174

Gnomad4 OTH

AF:

0.168

Alfa

AF:

0.177

Hom.:

4112

Bravo

AF:

0.183

Asia WGS

AF:

0.140

AC:

487

AN:

3478

EpiCase

AF:

0.177

EpiControl

AF:

0.174

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 15, 2018	- -

Epileptic encephalopathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.74

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