rs728293

Positions:

• chr4-47355666-G-A
• chr4-47355666-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000812.4(GABRB1):​c.544+35457G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,960 control chromosomes in the GnomAD database, including 13,376 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 0.41 (13376 hom., cov: 32)
• Consequence: GABRB1 NM_000812.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

Genes affected

GABRB1 (HGNC:4081): (gamma-aminobutyric acid type A receptor subunit beta1) The gamma-aminobutyric acid (GABA) A receptor is a multisubunit chloride channel that mediates the fastest inhibitory synaptic transmission in the central nervous system. This gene encodes GABA A receptor, beta 1 subunit. It is mapped to chromosome 4p12 in a cluster comprised of genes encoding alpha 4, alpha 2 and gamma 1 subunits of the GABA A receptor. Alteration of this gene is implicated in the pathogenetics of schizophrenia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABRB1	NM_000812.4	c.544+35457G>A		intron_variant		ENST00000295454.8	NP_000803.2
GABRB1	XM_024453976.2	c.445+35457G>A		intron_variant			XP_024309744.1
GABRB1	XM_024453977.2	c.445+35457G>A		intron_variant			XP_024309745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRB1	ENST00000295454.8	c.544+35457G>A		intron_variant		1	NM_000812.4	ENSP00000295454.3
GABRB1	ENST00000510909.1	n.*212+35457G>A		intron_variant		4		ENSP00000426766.1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62395 AN: 151840 Hom.: 13364 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.431

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.411 AC: 62436 AN: 151960 Hom.: 13376 Cov.: 32 AF XY: 0.400 AC XY: 29706 AN XY: 74284

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.427

Alfa AF: 0.440 Hom.: 4886

Bravo AF: 0.420

Asia WGS AF: 0.195 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	14
DANN	Benign	0.56

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

LitVar

Other links and lift over

dbSNP: rs728293; hg19: chr4-47357683;