rs7764923

Variant names:

• chr6-89313202-C-T
• rs7764923
• NM_002043.5:c.113+1851G>A

Variant summary

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

The NM_002043.5(GABRR2):​c.113+1851G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,116 control chromosomes in the GnomAD database, including 11,522 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 0.35 (11522 hom., cov: 32)
• Consequence: GABRR2 NM_002043.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 15 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRR2	NM_002043.5	c.113+1851G>A		intron_variant	Intron 1 of 8	ENST00000402938.4	NP_002034.3
GABRR2	XM_047418599.1	c.188+1851G>A		intron_variant	Intron 1 of 9		XP_047274555.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRR2	ENST00000402938.4	c.113+1851G>A		intron_variant	Intron 1 of 8	1	NM_002043.5	ENSP00000386029.4
GABRR2	ENST00000602808.1	n.247+1851G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52619 AN: 151998 Hom.: 11496 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.346 AC: 52703 AN: 152116 Hom.: 11522 Cov.: 32 AF XY: 0.344 AC XY: 25606 AN XY: 74382

African (AFR) AF: 0.622 AC: 25800 AN: 41476

American (AMR) AF: 0.277 AC: 4238 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3470

East Asian (EAS) AF: 0.192 AC: 996 AN: 5180

South Asian (SAS) AF: 0.369 AC: 1778 AN: 4824

European-Finnish (FIN) AF: 0.175 AC: 1853 AN: 10596

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15613 AN: 67984

Other (OTH) AF: 0.344 AC: 725 AN: 2106

Alfa AF: 0.278 Hom.: 8834

Bravo AF: 0.364

Asia WGS AF: 0.327 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.37
PhyloP100		0.085
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: rs7764923; hg19: chr6-90022921;