6-89299592-T-C

Position:

• chr6-89299592-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+167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,896 control chromosomes in the GnomAD database, including 27,440 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 0.59 (27440 hom., cov: 31)
• Consequence: GABRR2 NM_002043.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

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 (AMR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRR2	NM_002043.5	c.220+167A>G		intron_variant		ENST00000402938.4
GABRR2	XM_047418599.1	c.295+167A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRR2	ENST00000402938.4	c.220+167A>G		intron_variant		1	NM_002043.5	P1
GABRR2	ENST00000602808.1	n.354+167A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90085 AN: 151778 Hom.: 27426 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.593 AC: 90144 AN: 151896 Hom.: 27440 Cov.: 31 AF XY: 0.591 AC XY: 43904 AN XY: 74236

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.614

Alfa AF: 0.642 Hom.: 63814

Bravo AF: 0.600

Asia WGS AF: 0.594 AC: 2068 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	9.4
DANN	Benign	0.78

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: rs1570932; hg19: chr6-90009311;