rs11967322

Variant names:

• chr6-89200045-C-T
• rs11967322
• NM_002042.5:c.281-616G>A

Variant summary

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

The NM_002042.5(GABRR1):​c.281-616G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,748 control chromosomes in the GnomAD database, including 13,550 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 0.41 (13550 hom., cov: 30)
• Consequence: GABRR1 NM_002042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 1 publications found

Genes affected

GABRR1 (HGNC:4090): (gamma-aminobutyric acid type A receptor subunit rho1) GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA receptors, which are ligand-gated chloride channels. GABRR1 is a member of the rho subunit family. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRR1	NM_002042.5	c.281-616G>A		intron_variant	Intron 3 of 9	ENST00000454853.7	NP_002033.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRR1	ENST00000454853.7	c.281-616G>A		intron_variant	Intron 3 of 9	1	NM_002042.5	ENSP00000412673.2
GABRR1	ENST00000435811.5	c.230-616G>A		intron_variant	Intron 2 of 8	2		ENSP00000394687.1
GABRR1	ENST00000369451.7	c.20-616G>A		intron_variant	Intron 5 of 11	5		ENSP00000358463.3
GABRR1	ENST00000457434.1	n.*242-616G>A		intron_variant	Intron 4 of 10	5		ENSP00000410130.1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62820 AN: 151630 Hom.: 13525 Cov.: 30

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.414 AC: 62887 AN: 151748 Hom.: 13550 Cov.: 30 AF XY: 0.410 AC XY: 30404 AN XY: 74162

African (AFR) AF: 0.465 AC: 19209 AN: 41332

American (AMR) AF: 0.299 AC: 4555 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3470

East Asian (EAS) AF: 0.0709 AC: 366 AN: 5164

South Asian (SAS) AF: 0.323 AC: 1551 AN: 4800

European-Finnish (FIN) AF: 0.417 AC: 4378 AN: 10510

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30041 AN: 67900

Other (OTH) AF: 0.411 AC: 869 AN: 2112

Alfa AF: 0.438 Hom.: 3071

Bravo AF: 0.407

Asia WGS AF: 0.223 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.53
PhyloP100		-0.64
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: rs11967322; hg19: chr6-89909764;