rs6902106

Positions:

• chr6-89216021-A-C
• chr6-89216021-A-G

Variant summary

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

The ENST00000454853.7(GABRR1):​c.122+1180T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,054 control chromosomes in the GnomAD database, including 8,644 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 0.32 (8644 hom., cov: 32)
• Consequence: GABRR1 ENST00000454853.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABRR1	NM_002042.5	c.122+1180T>G		intron_variant		ENST00000454853.7	NP_002033.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRR1	ENST00000454853.7	c.122+1180T>G		intron_variant		1	NM_002042.5	ENSP00000412673	P1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48698 AN: 151936 Hom.: 8625 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0779

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.321 AC: 48758 AN: 152054 Hom.: 8644 Cov.: 32 AF XY: 0.317 AC XY: 23562 AN XY: 74344

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0777

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.269

Alfa AF: 0.273 Hom.: 3743

Bravo AF: 0.315

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.80

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: rs6902106; hg19: chr6-89925740;