rs9451194

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002043.5(GABRR2):​c.221-3938C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,960 control chromosomes in the GnomAD database, including 15,050 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 0.44 ( 15050 hom., cov: 33)

Consequence

GABRR2
NM_002043.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.897
Variant links:
Genes affected
GABRR2 (HGNC:4091): (gamma-aminobutyric acid type A receptor subunit rho2) Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA receptors, which are ligand-gated chloride channels. The protein encoded by this gene is a member of the rho subunit family and is a component of the GABA type A receptor complex. This gene exists on chromosome 6q next to the gene encoding the rho 1 subunit of the GABA type A receptor, in a region thought to be associated with susceptibility for psychiatric disorders and epilepsy. Polymorphisms in this gene may also be associated with alcohol dependence, and general cognitive ability. [provided by RefSeq, Apr 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GABRR2NM_002043.5 linkc.221-3938C>T intron_variant Intron 2 of 8 ENST00000402938.4 NP_002034.3 P28476-1
GABRR2XM_047418599.1 linkc.296-3938C>T intron_variant Intron 2 of 9 XP_047274555.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GABRR2ENST00000402938.4 linkc.221-3938C>T intron_variant Intron 2 of 8 1 NM_002043.5 ENSP00000386029.4 P28476-1
GABRR2ENST00000602808.1 linkn.355-3938C>T intron_variant Intron 2 of 3 3

Frequencies

GnomAD3 genomes
AF:
0.442
AC:
67168
AN:
151840
Hom.:
15035
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.389
Gnomad AMI
AF:
0.441
Gnomad AMR
AF:
0.465
Gnomad ASJ
AF:
0.377
Gnomad EAS
AF:
0.638
Gnomad SAS
AF:
0.524
Gnomad FIN
AF:
0.485
Gnomad MID
AF:
0.436
Gnomad NFE
AF:
0.444
Gnomad OTH
AF:
0.476
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.442
AC:
67229
AN:
151960
Hom.:
15050
Cov.:
33
AF XY:
0.446
AC XY:
33140
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.389
Gnomad4 AMR
AF:
0.466
Gnomad4 ASJ
AF:
0.377
Gnomad4 EAS
AF:
0.638
Gnomad4 SAS
AF:
0.523
Gnomad4 FIN
AF:
0.485
Gnomad4 NFE
AF:
0.444
Gnomad4 OTH
AF:
0.479
Alfa
AF:
0.443
Hom.:
23714
Bravo
AF:
0.440
Asia WGS
AF:
0.569
AC:
1980
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
5.5
DANN
Benign
0.74

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9451194; hg19: chr6-89985379; API