rs6930407

Variant names:

• chr6-89195520-G-A
• rs6930407
• NM_002042.5:c.572+2500C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-89195520-G-A
• chr6-89195520-G-T

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+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
• Publications: 5 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=-0.96).
• 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 rank	MANE	Protein	UniProt
GABRR1	NM_002042.5	c.572+2500C>T		intron_variant	Intron 5 of 9	ENST00000454853.7	NP_002033.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRR1	ENST00000454853.7	c.572+2500C>T		intron_variant	Intron 5 of 9	1	NM_002042.5	ENSP00000412673.2
GABRR1	ENST00000435811.5	c.521+2500C>T		intron_variant	Intron 4 of 8	2		ENSP00000394687.1
GABRR1	ENST00000369451.7	c.311+2500C>T		intron_variant	Intron 7 of 11	5		ENSP00000358463.3
GABRR1	ENST00000457434.1	n.*533+2500C>T		intron_variant	Intron 6 of 10	5		ENSP00000410130.1

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

African (AFR) AF: 0.240 AC: 9914 AN: 41242

American (AMR) AF: 0.0857 AC: 1297 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.0927 AC: 322 AN: 3472

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5160

South Asian (SAS) AF: 0.0736 AC: 353 AN: 4794

European-Finnish (FIN) AF: 0.179 AC: 1817 AN: 10132

Middle Eastern (MID) AF: 0.0862 AC: 25 AN: 290

European-Non Finnish (NFE) AF: 0.136 AC: 9246 AN: 67844

Other (OTH) AF: 0.134 AC: 281 AN: 2104

Alfa AF: 0.133 Hom.: 1811

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
PhyloP100		-2.0
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: rs6930407; hg19: chr6-89905239;