rs6942204

Variant names:

• chr6-89306249-T-C
• rs6942204
• NM_002043.5:c.114-6384A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002043.5(GABRR2):​c.114-6384A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,554 control chromosomes in the GnomAD database, including 11,304 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 0.37 (11304 hom., cov: 30)
• Consequence: GABRR2 NM_002043.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002043.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRR2	NM_002043.5	MANE Select	c.114-6384A>G		intron	N/A	NP_002034.3	P28476-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRR2	ENST00000402938.4	TSL:1 MANE Select	c.114-6384A>G		intron	N/A	ENSP00000386029.4	P28476-1
	GABRR2	ENST00000602808.1	TSL:3	n.248-6384A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55662 AN: 151436 Hom.: 11280 Cov.: 30

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.368 AC: 55740 AN: 151554 Hom.: 11304 Cov.: 30 AF XY: 0.373 AC XY: 27599 AN XY: 74016

African (AFR) AF: 0.541 AC: 22321 AN: 41234

American (AMR) AF: 0.281 AC: 4281 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1964 AN: 5156

South Asian (SAS) AF: 0.391 AC: 1872 AN: 4784

European-Finnish (FIN) AF: 0.382 AC: 3998 AN: 10474

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18999 AN: 67896

Other (OTH) AF: 0.351 AC: 738 AN: 2102

Alfa AF: 0.306 Hom.: 3701

Bravo AF: 0.364

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.29
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6942204; hg19: chr6-90015968;