rs11967322

Variant summary

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

The NM_002042.5(GABRR1):​c.281-616G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,748 control chromosomes in the GnomAD database, including 13,550 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 0.41 ( 13550 hom., cov: 30)

Consequence

GABRR1
NM_002042.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.638
Variant links:
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]

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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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GABRR1NM_002042.5 linkuse as main transcriptc.281-616G>A intron_variant ENST00000454853.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GABRR1ENST00000454853.7 linkuse as main transcriptc.281-616G>A intron_variant 1 NM_002042.5 P1P24046-1
GABRR1ENST00000369451.7 linkuse as main transcriptc.20-616G>A intron_variant 5 P24046-3
GABRR1ENST00000435811.5 linkuse as main transcriptc.230-616G>A intron_variant 2 P24046-2
GABRR1ENST00000457434.1 linkuse as main transcriptc.*242-616G>A intron_variant, NMD_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.414
AC:
62820
AN:
151630
Hom.:
13525
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.464
Gnomad AMI
AF:
0.344
Gnomad AMR
AF:
0.299
Gnomad ASJ
AF:
0.428
Gnomad EAS
AF:
0.0709
Gnomad SAS
AF:
0.323
Gnomad FIN
AF:
0.417
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.442
Gnomad OTH
AF:
0.412
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.414
AC:
62887
AN:
151748
Hom.:
13550
Cov.:
30
AF XY:
0.410
AC XY:
30404
AN XY:
74162
show subpopulations
Gnomad4 AFR
AF:
0.465
Gnomad4 AMR
AF:
0.299
Gnomad4 ASJ
AF:
0.428
Gnomad4 EAS
AF:
0.0709
Gnomad4 SAS
AF:
0.323
Gnomad4 FIN
AF:
0.417
Gnomad4 NFE
AF:
0.442
Gnomad4 OTH
AF:
0.411
Alfa
AF:
0.437
Hom.:
2983
Bravo
AF:
0.407
Asia WGS
AF:
0.223
AC:
779
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
0.56
DANN
Benign
0.53

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: rs11967322; hg19: chr6-89909764; API