rs964626

chr6-89289577-T-C

Variant summary

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

The NM_002043.5(GABRR2):c.220+10182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,956 control chromosomes in the GnomAD database, including 4,318 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 0.23 (4318 hom., cov: 32)
• Consequence: GABRR2 NM_002043.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRR2	NM_002043.5	c.220+10182A>G		intron_variant		ENST00000402938.4
GABRR2	XM_047418599.1	c.295+10182A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRR2	ENST00000402938.4	c.220+10182A>G		intron_variant		1	NM_002043.5	P1
GABRR2	ENST00000602808.1	n.354+10182A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35626 AN: 151838 Hom.: 4316 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.235 AC: 35646 AN: 151956 Hom.: 4318 Cov.: 32 AF XY: 0.238 AC XY: 17645 AN XY: 74268

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.218

Alfa AF: 0.223 Hom.: 3795

Bravo AF: 0.227

Asia WGS AF: 0.404 AC: 1402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.8
Dann	Benign	0.74

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

Other links and lift over

dbSNP: rs964626; hg19: chr6-89999296; COSMIC: COSV68766137;