6-89195453-A-G

Variant names:

• chr6-89195453-A-G
• rs9451177
• NM_002042.5:c.572+2567T>C

Variant summary

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

The NM_002042.5(GABRR1):​c.572+2567T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 148,990 control chromosomes in the GnomAD database, including 5,375 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 0.26 (5375 hom., cov: 30)
• Consequence: GABRR1 NM_002042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002042.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRR1	NM_002042.5	MANE Select	c.572+2567T>C		intron	N/A	NP_002033.2
	GABRR1	NM_001256703.1		c.521+2567T>C		intron	N/A	NP_001243632.1
	GABRR1	NM_001256704.1		c.311+2567T>C		intron	N/A	NP_001243633.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRR1	ENST00000454853.7	TSL:1 MANE Select	c.572+2567T>C		intron	N/A	ENSP00000412673.2
	GABRR1	ENST00000435811.5	TSL:2	c.521+2567T>C		intron	N/A	ENSP00000394687.1
	GABRR1	ENST00000369451.7	TSL:5	c.311+2567T>C		intron	N/A	ENSP00000358463.3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39181 AN: 148894 Hom.: 5371 Cov.: 30

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.263 AC: 39205 AN: 148990 Hom.: 5375 Cov.: 30 AF XY: 0.259 AC XY: 18809 AN XY: 72588

African (AFR) AF: 0.243 AC: 9824 AN: 40370

American (AMR) AF: 0.205 AC: 3045 AN: 14850

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 894 AN: 3450

East Asian (EAS) AF: 0.0318 AC: 160 AN: 5026

South Asian (SAS) AF: 0.292 AC: 1369 AN: 4690

European-Finnish (FIN) AF: 0.263 AC: 2646 AN: 10048

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20393 AN: 67286

Other (OTH) AF: 0.263 AC: 544 AN: 2072

Alfa AF: 0.272 Hom.: 767

Bravo AF: 0.249

Asia WGS AF: 0.193 AC: 675 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.35
PhyloP100		0.24
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: rs9451177; hg19: chr6-89905172;