chr4-46057233-C-T
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.916+984G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,900 control chromosomes in the GnomAD database, including 19,823 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 0.50 ( 19823 hom., cov: 32)
Consequence
GABRG1
NM_173536.4 intron
NM_173536.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.32
Publications
10 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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.503 AC: 76401AN: 151782Hom.: 19796 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
76401
AN:
151782
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: 0.504 AC: 76494AN: 151900Hom.: 19823 Cov.: 32 AF XY: 0.503 AC XY: 37309AN XY: 74226 show subpopulations
GnomAD4 genome
AF:
AC:
76494
AN:
151900
Hom.:
Cov.:
32
AF XY:
AC XY:
37309
AN XY:
74226
show subpopulations
African (AFR)
AF:
AC:
25637
AN:
41468
American (AMR)
AF:
AC:
7186
AN:
15234
Ashkenazi Jewish (ASJ)
AF:
AC:
1457
AN:
3470
East Asian (EAS)
AF:
AC:
1849
AN:
5142
South Asian (SAS)
AF:
AC:
1570
AN:
4820
European-Finnish (FIN)
AF:
AC:
5880
AN:
10546
Middle Eastern (MID)
AF:
AC:
99
AN:
294
European-Non Finnish (NFE)
AF:
AC:
31311
AN:
67914
Other (OTH)
AF:
AC:
993
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1920
3840
5761
7681
9601
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
670
1340
2010
2680
3350
<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:
1358
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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