Variant chr9-98290277-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005458.8(GABBR2):c.*307A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 125,612 control chromosomes in the GnomAD database, including 800 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 800 hom., cov: 29)

Exomes 𝑓: 0.0094 ( 2 hom. )

Failed GnomAD Quality Control

Consequence

GABBR2
NM_005458.8 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0650

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 9-98290277-T-G is Benign according to our data. Variant chr9-98290277-T-G is described in ClinVar as [Benign]. Clinvar id is 1182606.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
GABBR2	NM_005458.8 linkuse as main transcript	c.*307A>C	3_prime_UTR_variant	19/19	ENST00000259455.4
GABBR2	XM_005252316.6 linkuse as main transcript	c.*307A>C	3_prime_UTR_variant	17/17
GABBR2	XM_017015331.3 linkuse as main transcript	c.*307A>C	3_prime_UTR_variant	18/18
GABBR2	XM_017015332.3 linkuse as main transcript	c.*307A>C	3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABBR2	ENST00000259455.4 linkuse as main transcript	c.*307A>C		3_prime_UTR_variant	19/19	1	NM_005458.8	P1

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

16502

AN:

125592

Hom.:

800

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0463

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.122

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.130

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00939

AC:

142

AN:

15130

Hom.:

Cov.:

AF XY:

0.00965

AC XY:

AN XY:

7768

show subpopulations

Gnomad4 AFR exome

AF:

0.00120

Gnomad4 AMR exome

AF:

0.0113

Gnomad4 ASJ exome

AF:

0.00436

Gnomad4 EAS exome

AF:

0.00459

Gnomad4 SAS exome

AF:

0.00714

Gnomad4 FIN exome

AF:

0.0239

Gnomad4 NFE exome

AF:

0.00950

Gnomad4 OTH exome

AF:

0.0110

GnomAD4 genome

AF:

0.131

AC:

16496

AN:

125612

Hom.:

800

Cov.:

AF XY:

0.128

AC XY:

7773

AN XY:

60648

show subpopulations

Gnomad4 AFR

AF:

0.0462

Gnomad4 AMR

AF:

0.140

Gnomad4 ASJ

AF:

0.109

Gnomad4 EAS

AF:

0.145

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.163

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.0364

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.4

DANN

Benign

0.73

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