Variant chr5-161293870-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001371727.1(GABRB2):c.*211C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 545,512 control chromosomes in the GnomAD database, including 244 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 47 hom., cov: 32)

Exomes 𝑓: 0.028 ( 197 hom. )

Consequence

GABRB2
NM_001371727.1 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.430

Variant links:

Genes affected

GABRB2 (HGNC:4082): (gamma-aminobutyric acid type A receptor subunit beta2) 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 2 subunit. It is mapped to chromosome 5q34 in a cluster comprised of genes encoding alpha 1 and gamma 2 subunits of the GABA A receptor. Alternative splicing of this gene generates 2 transcript variants, differing by a 114 bp insertion. [provided by RefSeq, Jul 2008]

GABRB2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 5-161293870-G-A is Benign according to our data. Variant chr5-161293870-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1217644.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0222 (3373/152242) while in subpopulation NFE AF= 0.0357 (2425/68002). AF 95% confidence interval is 0.0345. There are 47 homozygotes in gnomad4. There are 1557 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 3373 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
GABRB2	NM_001371727.1 linkuse as main transcript	c.*211C>T	3_prime_UTR_variant	10/10	ENST00000393959.6
GABRB2	NM_000813.3 linkuse as main transcript	c.*211C>T	3_prime_UTR_variant	10/10
GABRB2	NM_021911.3 linkuse as main transcript	c.*211C>T	3_prime_UTR_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRB2	ENST00000393959.6 linkuse as main transcript	c.*211C>T		3_prime_UTR_variant	10/10	1	NM_001371727.1		P47870-2

Frequencies

GnomAD3 genomes

AF:

0.0222

AC:

3373

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00649

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0199

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00973

Gnomad FIN

AF:

0.0202

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0357

Gnomad OTH

AF:

0.0272

GnomAD4 exome

AF:

0.0280

AC:

10996

AN:

393270

Hom.:

197

Cov.:

AF XY:

0.0275

AC XY:

5633

AN XY:

204642

show subpopulations

Gnomad4 AFR exome

AF:

0.00706

Gnomad4 AMR exome

AF:

0.0186

Gnomad4 ASJ exome

AF:

0.0169

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00988

Gnomad4 FIN exome

AF:

0.0223

Gnomad4 NFE exome

AF:

0.0367

Gnomad4 OTH exome

AF:

0.0295

GnomAD4 genome

AF:

0.0222

AC:

3373

AN:

152242

Hom.:

Cov.:

AF XY:

0.0209

AC XY:

1557

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00647

Gnomad4 AMR

AF:

0.0198

Gnomad4 ASJ

AF:

0.0133

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.00974

Gnomad4 FIN

AF:

0.0202

Gnomad4 NFE

AF:

0.0357

Gnomad4 OTH

AF:

0.0274

Alfa

AF:

0.0206

Hom.:

Bravo

AF:

0.0217

Asia WGS

AF:

0.00549

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

4.2

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over