Variant rs12520992 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_198904.4(GABRG2):c.922+108A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,150,928 control chromosomes in the GnomAD database, including 9,481 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.089 ( 810 hom., cov: 32)

Exomes 𝑓: 0.12 ( 8671 hom. )

Consequence

GABRG2
NM_198904.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.550

Variant links:

Genes affected

GABRG2 (HGNC:4087): (gamma-aminobutyric acid type A receptor subunit gamma2) This gene encodes a gamma-aminobutyric acid (GABA) receptor. GABA is the major inhibitory neurotransmitter in the mammlian brain, where it acts at GABA-A receptors, which are ligand-gated chloride channels. GABA-A receptors are pentameric, consisting of proteins from several subunit classes: alpha, beta, gamma, delta and rho. Mutations in this gene have been associated with epilepsy and febrile seizures. Multiple transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

GABRG2 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=-0.87).

BP6

Variant 5-162142424-A-C is Benign according to our data. Variant chr5-162142424-A-C is described in ClinVar as [Benign]. Clinvar id is 675186.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRG2	NM_198904.4 linkuse as main transcript	c.922+108A>C		intron_variant		ENST00000639213.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRG2	ENST00000639213.2 linkuse as main transcript	c.922+108A>C		intron_variant		1	NM_198904.4	A1	P18507-2

Frequencies

GnomAD3 genomes

AF:

0.0893

AC:

13590

AN:

152158

Hom.:

810

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0273

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0800

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.00308

Gnomad SAS

AF:

0.0748

Gnomad FIN

AF:

0.0929

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.136

Gnomad OTH

AF:

0.0910

GnomAD4 exome

AF:

0.124

AC:

123528

AN:

998652

Hom.:

8671

Cov.:

AF XY:

0.122

AC XY:

63098

AN XY:

515372

show subpopulations

Gnomad4 AFR exome

AF:

0.0240

Gnomad4 AMR exome

AF:

0.0551

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.00168

Gnomad4 SAS exome

AF:

0.0773

Gnomad4 FIN exome

AF:

0.0961

Gnomad4 NFE exome

AF:

0.145

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.0893

AC:

13596

AN:

152276

Hom.:

810

Cov.:

AF XY:

0.0860

AC XY:

6407

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0273

Gnomad4 AMR

AF:

0.0799

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.00308

Gnomad4 SAS

AF:

0.0755

Gnomad4 FIN

AF:

0.0929

Gnomad4 NFE

AF:

0.136

Gnomad4 OTH

AF:

0.0910

Alfa

AF:

0.0335

Hom.:

Bravo

AF:

0.0862

Asia WGS

AF:

0.0420

AC:

147

AN:

3478

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

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.5

DANN

Benign

0.68

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