3-98020827-C-T

Variant summary

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

The NM_001105580.3(GABRR3):​c.239-3105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,200 control chromosomes in the GnomAD database, including 6,194 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 0.26 ( 6194 hom., cov: 30)

Consequence

GABRR3
NM_001105580.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.728
Variant links:
Genes affected
GABRR3 (HGNC:17969): (gamma-aminobutyric acid type A receptor subunit rho3) The neurotransmitter gamma-aminobutyric acid (GABA) functions in the central nervous system to regulate synaptic transmission of neurons. This gene encodes one of three related subunits, which combine as homo- or hetero-pentamers to form GABA(C) receptors. In humans, some individuals contain a single-base polymorphism (dbSNP rs832032) that is predicted to inactivate the gene product. [provided by RefSeq, Jan 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GABRR3NM_001105580.3 linkc.239-3105G>A intron_variant Intron 3 of 9 ENST00000472788.6 NP_001099050.1 A8MPY1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GABRR3ENST00000472788.6 linkc.239-3105G>A intron_variant Intron 3 of 9 5 NM_001105580.3 ENSP00000420790.1 A8MPY1
GABRR3ENST00000470589.1 linkn.356-3105G>A intron_variant Intron 3 of 5 1

Frequencies

GnomAD3 genomes
AF:
0.261
AC:
39447
AN:
151100
Hom.:
6197
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0766
Gnomad AMI
AF:
0.220
Gnomad AMR
AF:
0.298
Gnomad ASJ
AF:
0.282
Gnomad EAS
AF:
0.436
Gnomad SAS
AF:
0.363
Gnomad FIN
AF:
0.370
Gnomad MID
AF:
0.196
Gnomad NFE
AF:
0.327
Gnomad OTH
AF:
0.270
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.261
AC:
39439
AN:
151200
Hom.:
6194
Cov.:
30
AF XY:
0.265
AC XY:
19569
AN XY:
73800
show subpopulations
Gnomad4 AFR
AF:
0.0766
Gnomad4 AMR
AF:
0.299
Gnomad4 ASJ
AF:
0.282
Gnomad4 EAS
AF:
0.435
Gnomad4 SAS
AF:
0.363
Gnomad4 FIN
AF:
0.370
Gnomad4 NFE
AF:
0.327
Gnomad4 OTH
AF:
0.270
Alfa
AF:
0.257
Hom.:
825
Bravo
AF:
0.244
Asia WGS
AF:
0.364
AC:
1267
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.4
DANN
Benign
0.59

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: rs854580; hg19: chr3-97739671; API