GeneBe

rs693547

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000807.4(GABRA2):​c.1060-3936T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 30)
Failed GnomAD Quality Control

Consequence

GABRA2
NM_000807.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.358

Publications

5 publications found
Variant links:
Genes affected
GABRA2 (HGNC:4076): (gamma-aminobutyric acid type A receptor subunit alpha2) GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA-A receptors, which are ligand-gated chloride channels. Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. At least 16 distinct subunits of GABA-A receptors have been identified. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]
GABRA2 Gene-Disease associations (from GenCC):
  • developmental and epileptic encephalopathy, 78
    Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
  • undetermined early-onset epileptic encephalopathy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000807.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GABRA2
NM_000807.4
MANE Select
c.1060-3936T>G
intron
N/ANP_000798.2
GABRA2
NM_001330690.2
c.1239+1655T>G
intron
N/ANP_001317619.1
GABRA2
NM_001377144.1
c.1239+1655T>G
intron
N/ANP_001364073.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GABRA2
ENST00000381620.9
TSL:1 MANE Select
c.1060-3936T>G
intron
N/AENSP00000371033.4
GABRA2
ENST00000507069.5
TSL:3
c.1239+1655T>G
intron
N/AENSP00000427603.1
GABRA2
ENST00000356504.5
TSL:2
c.1060-3936T>G
intron
N/AENSP00000348897.1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151050
Hom.:
0
Cov.:
30
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
151050
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
73684
African (AFR)
AF:
0.00
AC:
0
AN:
41202
American (AMR)
AF:
0.00
AC:
0
AN:
15066
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3456
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5118
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4816
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10550
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67544
Other (OTH)
AF:
0.00
AC:
0
AN:
2072
Alfa
AF:
0.00
Hom.:
1054

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.63
DANN
Benign
0.20
PhyloP100
-0.36

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

Other links and lift over

dbSNP: rs693547; hg19: chr4-46256557; API