rs6930407

chr6-89195520-G-Achr6-89195520-G-T

Variant summary

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

The NM_002042.5(GABRR1):c.572+2500C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 151,092 control chromosomes in the GnomAD database, including 2,085 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 0.15 (2085 hom., cov: 32)
• Consequence: GABRR1 NM_002042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRR1	NM_002042.5	c.572+2500C>T		intron_variant		ENST00000454853.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRR1	ENST00000454853.7	c.572+2500C>T		intron_variant		1	NM_002042.5	P1
GABRR1	ENST00000369451.7	c.311+2500C>T		intron_variant		5
GABRR1	ENST00000435811.5	c.521+2500C>T		intron_variant		2
GABRR1	ENST00000457434.1	c.*533+2500C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23355 AN: 151006 Hom.: 2075 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0927

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.155 AC: 23403 AN: 151092 Hom.: 2085 Cov.: 32 AF XY: 0.154 AC XY: 11343 AN XY: 73698

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.0857

Gnomad4 ASJ AF: 0.0927

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0736

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.134

Alfa AF: 0.129 Hom.: 1277

Bravo AF: 0.151

Asia WGS AF: 0.0780 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.4
Dann	Benign	0.40

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: rs6930407; hg19: chr6-89905239;