rs407221

chr6-89180656-C-T

Variant summary

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

The NM_002042.5(GABRR1):c.950-168G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,090 control chromosomes in the GnomAD database, including 49,241 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 0.80 (49241 hom., cov: 30)
• Consequence: GABRR1 NM_002042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRR1	NM_002042.5	c.950-168G>A		intron_variant		ENST00000454853.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRR1	ENST00000454853.7	c.950-168G>A		intron_variant		1	NM_002042.5	P1
GABRR1	ENST00000369451.7	c.689-168G>A		intron_variant		5
GABRR1	ENST00000435811.5	c.899-168G>A		intron_variant		2
GABRR1	ENST00000457434.1	c.*911-168G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121480 AN: 151972 Hom.: 49193 Cov.: 30

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.799 AC: 121589 AN: 152090 Hom.: 49241 Cov.: 30 AF XY: 0.800 AC XY: 59452 AN XY: 74324

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.779

Alfa AF: 0.740 Hom.: 84033

Bravo AF: 0.812

Asia WGS AF: 0.839 AC: 2920 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	0.014
Dann	Benign	0.70

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: rs407221; hg19: chr6-89890375;