4-46992955-GAA-GAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_000809.4(GABRA4):​c.87-12_87-10dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00044 ( 0 hom. )

Consequence

GABRA4
NM_000809.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0260
Variant links:
Genes affected
GABRA4 (HGNC:4078): (gamma-aminobutyric acid type A receptor subunit alpha4) Gamma-aminobutyric acid (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. This gene encodes subunit alpha-4, which is involved in the etiology of autism and eventually increases autism risk through interaction with another subunit, gamma-aminobutyric acid receptor beta-1 (GABRB1). Alternatively spliced transcript variants encoding different isoforms have been found in this gene.[provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 21 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GABRA4NM_000809.4 linkc.87-12_87-10dupTTT intron_variant ENST00000264318.4 NP_000800.2 P48169X5D7F5
GABRA4NM_001204266.2 linkc.30-12_30-10dupTTT intron_variant NP_001191195.1 P48169
GABRA4NM_001204267.2 linkc.30-12_30-10dupTTT intron_variant NP_001191196.1 P48169

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GABRA4ENST00000264318.4 linkc.87-10_87-9insTTT intron_variant 1 NM_000809.4 ENSP00000264318.3 P48169

Frequencies

GnomAD3 genomes
AF:
0.000118
AC:
17
AN:
144084
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000230
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000206
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000407
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000234
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000152
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000438
AC:
506
AN:
1155902
Hom.:
0
Cov.:
19
AF XY:
0.000416
AC XY:
243
AN XY:
584678
show subpopulations
Gnomad4 AFR exome
AF:
0.000866
Gnomad4 AMR exome
AF:
0.000434
Gnomad4 ASJ exome
AF:
0.000221
Gnomad4 EAS exome
AF:
0.000473
Gnomad4 SAS exome
AF:
0.000228
Gnomad4 FIN exome
AF:
0.000127
Gnomad4 NFE exome
AF:
0.000467
Gnomad4 OTH exome
AF:
0.000345
GnomAD4 genome
AF:
0.000146
AC:
21
AN:
144140
Hom.:
0
Cov.:
0
AF XY:
0.000158
AC XY:
11
AN XY:
69730
show subpopulations
Gnomad4 AFR
AF:
0.000306
Gnomad4 AMR
AF:
0.000206
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000409
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000234
Gnomad4 NFE
AF:
0.0000152
Gnomad4 OTH
AF:
0.000501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs3215202; hg19: chr4-46994972; API