chr4-47164764-T-G

Position:

• chr4-47164764-T-G

Variant summary

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

The NM_000812.4(GABRB1):​c.461+3295T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,080 control chromosomes in the GnomAD database, including 55,881 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 0.86 (55881 hom., cov: 32)
• Consequence: GABRB1 NM_000812.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABRB1	NM_000812.4	c.461+3295T>G		intron_variant		ENST00000295454.8	NP_000803.2
GABRB1	XM_017007986.3	c.461+3295T>G		intron_variant			XP_016863475.1
GABRB1	XM_024453976.2	c.362+3295T>G		intron_variant			XP_024309744.1
GABRB1	XM_024453977.2	c.362+3295T>G		intron_variant			XP_024309745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRB1	ENST00000295454.8	c.461+3295T>G		intron_variant		1	NM_000812.4	ENSP00000295454	P1
GABRB1	ENST00000510909.1	c.*129+3295T>G		intron_variant, NMD_transcript_variant		4		ENSP00000426766

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130193 AN: 151962 Hom.: 55849 Cov.: 32

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.857 AC: 130282 AN: 152080 Hom.: 55881 Cov.: 32 AF XY: 0.856 AC XY: 63603 AN XY: 74310

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.872

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.867

Alfa AF: 0.842 Hom.: 49700

Bravo AF: 0.863

Asia WGS AF: 0.855 AC: 2974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.43

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: rs989808; hg19: chr4-47166781;