rs12216134

Variant names:

• chr6-89210107-C-A
• rs12216134
• NM_002042.5:c.123-6622G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-89210107-C-A
• chr6-89210107-C-G
• chr6-89210107-C-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.123-6622G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 151,092 control chromosomes in the GnomAD database, including 210 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 0.053 (210 hom., cov: 31)
• Consequence: GABRR1 NM_002042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRR1	NM_002042.5	c.123-6622G>T		intron_variant	Intron 1 of 9	ENST00000454853.7	NP_002033.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRR1	ENST00000454853.7	c.123-6622G>T		intron_variant	Intron 1 of 9	1	NM_002042.5	ENSP00000412673.2

Frequencies

GnomAD3 genomes AF: 0.0527 AC: 7956 AN: 151022 Hom.: 211 Cov.: 31

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.0387

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0527 AC: 7963 AN: 151092 Hom.: 210 Cov.: 31 AF XY: 0.0527 AC XY: 3885 AN XY: 73730

African (AFR) AF: 0.0665 AC: 2731 AN: 41098

American (AMR) AF: 0.0360 AC: 547 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.0188 AC: 65 AN: 3466

East Asian (EAS) AF: 0.0269 AC: 138 AN: 5136

South Asian (SAS) AF: 0.0493 AC: 236 AN: 4788

European-Finnish (FIN) AF: 0.0743 AC: 759 AN: 10210

Middle Eastern (MID) AF: 0.0387 AC: 11 AN: 284

European-Non Finnish (NFE) AF: 0.0492 AC: 3339 AN: 67904

Other (OTH) AF: 0.0442 AC: 93 AN: 2104

Alfa AF: 0.0459 Hom.: 319

Bravo AF: 0.0501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.56
PhyloP100		0.41
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: rs12216134; hg19: chr6-89919826;