Variant 4-46992955-GAA-GAAAAA details in Genebe, Genetics Data Aggregator

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]

GABRA4 links:

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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	Effect	MANE	Protein	UniProt
GABRA4	NM_000809.4 link	c.87-12_87-10dupTTT	intron_variant	ENST00000264318.4	NP_000800.2	P48169X5D7F5
GABRA4	NM_001204266.2 link	c.30-12_30-10dupTTT	intron_variant		NP_001191195.1	P48169
GABRA4	NM_001204267.2 link	c.30-12_30-10dupTTT	intron_variant		NP_001191196.1	P48169

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRA4	ENST00000264318.4 link	c.87-10_87-9insTTT		intron_variant		1	NM_000809.4	ENSP00000264318.3		P48169

Frequencies

GnomAD3 genomes

AF:

0.000118

AC:

AN:

144084

Hom.:

Cov.:

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.:

Cov.:

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:

AN:

144140

Hom.:

Cov.:

AF XY:

0.000158

AC XY:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over