Variant chr9-98290276-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_005458.8(GABBR2):c.*308A>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 0.00514 in 94,938 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0051 ( 1 hom., cov: 27)

Exomes 𝑓: 0.0035 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

GABBR2
NM_005458.8 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 9-98290276-T-G is Benign according to our data. Variant chr9-98290276-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 1206699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 488 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
GABBR2	NM_005458.8 linkuse as main transcript	c.*308A>C	3_prime_UTR_variant	19/19	ENST00000259455.4
GABBR2	XM_005252316.6 linkuse as main transcript	c.*308A>C	3_prime_UTR_variant	17/17
GABBR2	XM_017015331.3 linkuse as main transcript	c.*308A>C	3_prime_UTR_variant	18/18
GABBR2	XM_017015332.3 linkuse as main transcript	c.*308A>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.*308A>C		3_prime_UTR_variant	19/19	1	NM_005458.8	P1

Frequencies

GnomAD3 genomes

AF:

0.00515

AC:

489

AN:

94920

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0104

Gnomad AMI

AF:

0.00156

Gnomad AMR

AF:

0.00192

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00521

Gnomad SAS

AF:

0.00335

Gnomad FIN

AF:

0.00293

Gnomad MID

AF:

0.0168

Gnomad NFE

AF:

0.00433

Gnomad OTH

AF:

0.00570

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00350

AC:

AN:

14286

Hom.:

Cov.:

AF XY:

0.00363

AC XY:

AN XY:

7448

show subpopulations

Gnomad4 AFR exome

AF:

0.00128

Gnomad4 AMR exome

AF:

0.00483

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00293

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0192

Gnomad4 NFE exome

AF:

0.00248

Gnomad4 OTH exome

AF:

0.00210

GnomAD4 genome

AF:

0.00514

AC:

488

AN:

94938

Hom.:

Cov.:

AF XY:

0.00475

AC XY:

220

AN XY:

46332

show subpopulations

Gnomad4 AFR

AF:

0.0103

Gnomad4 AMR

AF:

0.00201

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.00523

Gnomad4 SAS

AF:

0.00306

Gnomad4 FIN

AF:

0.00293

Gnomad4 NFE

AF:

0.00434

Gnomad4 OTH

AF:

0.00567

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.2

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