rs1497570
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173536.4(GABRG1):c.1132-3763G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,900 control chromosomes in the GnomAD database, including 20,011 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 0.51 ( 20011 hom., cov: 32)
Consequence
GABRG1
NM_173536.4 intron
NM_173536.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.611
Publications
4 publications found
Genes affected
GABRG1 (HGNC:4086): (gamma-aminobutyric acid type A receptor subunit gamma1) The protein encoded by this gene belongs to the ligand-gated ionic channel family. It is an integral membrane protein and plays an important role in inhibiting neurotransmission by binding to the benzodiazepine receptor and opening an integral chloride channel. This gene is clustered with three other family members on chromosome 4. [provided by RefSeq, Jul 2008]
GABRG1 Gene-Disease associations (from GenCC):
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: LIMITED Submitted by: G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.505 AC: 76700AN: 151784Hom.: 19975 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
76700
AN:
151784
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.506 AC: 76806AN: 151900Hom.: 20011 Cov.: 32 AF XY: 0.505 AC XY: 37448AN XY: 74214 show subpopulations
GnomAD4 genome
AF:
AC:
76806
AN:
151900
Hom.:
Cov.:
32
AF XY:
AC XY:
37448
AN XY:
74214
show subpopulations
African (AFR)
AF:
AC:
25918
AN:
41464
American (AMR)
AF:
AC:
7183
AN:
15206
Ashkenazi Jewish (ASJ)
AF:
AC:
1469
AN:
3466
East Asian (EAS)
AF:
AC:
1845
AN:
5142
South Asian (SAS)
AF:
AC:
1582
AN:
4816
European-Finnish (FIN)
AF:
AC:
5870
AN:
10554
Middle Eastern (MID)
AF:
AC:
99
AN:
294
European-Non Finnish (NFE)
AF:
AC:
31328
AN:
67940
Other (OTH)
AF:
AC:
998
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1939
3879
5818
7758
9697
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
672
1344
2016
2688
3360
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1380
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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