rs3734198

chr6-89254573-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002043.5(GABRR2):c.*3097C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 152,076 control chromosomes in the GnomAD database, including 29,432 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.60 (29432 hom., cov: 32)
• Consequence: GABRR2 NM_002043.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

Genes affected

GABRR2 (HGNC:4091): (gamma-aminobutyric acid type A receptor subunit rho2) Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA receptors, which are ligand-gated chloride channels. The protein encoded by this gene is a member of the rho subunit family and is a component of the GABA type A receptor complex. This gene exists on chromosome 6q next to the gene encoding the rho 1 subunit of the GABA type A receptor, in a region thought to be associated with susceptibility for psychiatric disorders and epilepsy. Polymorphisms in this gene may also be associated with alcohol dependence, and general cognitive ability. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRR2	NM_002043.5	c.*3097C>T		3_prime_UTR_variant	9/9	ENST00000402938.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRR2	ENST00000402938.4	c.*3097C>T		3_prime_UTR_variant	9/9	1	NM_002043.5	P1

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91452 AN: 151958 Hom.: 29390 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.556

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.602 AC: 91538 AN: 152076 Hom.: 29432 Cov.: 32 AF XY: 0.592 AC XY: 43999 AN XY: 74316

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.553

Alfa AF: 0.582 Hom.: 16690

Bravo AF: 0.598

Asia WGS AF: 0.378 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3734198; hg19: chr6-89964292;