4-47143090-C-T

Position:

• chr4-47143090-C-T

Variant summary

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

The NM_000812.4(GABRB1):​c.241-18159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 151,768 control chromosomes in the GnomAD database, including 61,521 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 0.90 (61521 hom., cov: 30)
• Consequence: GABRB1 NM_000812.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GABRB1	NM_000812.4	c.241-18159C>T		intron_variant		ENST00000295454.8	NP_000803.2
GABRB1	XM_024453976.2	c.142-18159C>T		intron_variant			XP_024309744.1
GABRB1	XM_024453977.2	c.142-18159C>T		intron_variant			XP_024309745.1
GABRB1	XM_017007986.3	c.241-18159C>T		intron_variant			XP_016863475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GABRB1	ENST00000295454.8	c.241-18159C>T		intron_variant		1	NM_000812.4	ENSP00000295454.3
GABRB1	ENST00000513567.5	c.142-18159C>T		intron_variant		4		ENSP00000426753.1
GABRB1	ENST00000510909.1	n.173-18159C>T		intron_variant		4		ENSP00000426766.1

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136471 AN: 151650 Hom.: 61475 Cov.: 30

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.900 AC: 136573 AN: 151768 Hom.: 61521 Cov.: 30 AF XY: 0.903 AC XY: 66941 AN XY: 74160

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.891

Alfa AF: 0.902 Hom.: 10455

Bravo AF: 0.895

Asia WGS AF: 0.868 AC: 3021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.47

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: rs7680321; hg19: chr4-47145107;