Variant 3-119947419-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001146156.2(GSK3B):c.283-68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0893 in 962,868 control chromosomes in the GnomAD database, including 4,678 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1115 hom., cov: 32)

Exomes 𝑓: 0.085 ( 3563 hom. )

Consequence

GSK3B
NM_001146156.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0280

Variant links:

Genes affected

GSK3B (HGNC:4617): (glycogen synthase kinase 3 beta) The protein encoded by this gene is a serine-threonine kinase belonging to the glycogen synthase kinase subfamily. It is a negative regulator of glucose homeostasis and is involved in energy metabolism, inflammation, ER-stress, mitochondrial dysfunction, and apoptotic pathways. Defects in this gene have been associated with Parkinson disease and Alzheimer disease. [provided by RefSeq, Aug 2017]

GSK3B 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=-0.81).

BP6

Variant 3-119947419-C-T is Benign according to our data. Variant chr3-119947419-C-T is described in ClinVar as [Benign]. Clinvar id is 1227109.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
GSK3B	NM_001146156.2 linkuse as main transcript	c.283-68G>A	intron_variant	ENST00000264235.13
GSK3B	NM_001354596.2 linkuse as main transcript	c.283-68G>A	intron_variant
GSK3B	NM_002093.4 linkuse as main transcript	c.283-68G>A	intron_variant
GSK3B	XM_006713610.4 linkuse as main transcript	c.283-68G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSK3B	ENST00000264235.13 linkuse as main transcript	c.283-68G>A		intron_variant		1	NM_001146156.2	A1	P49841-1

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

16960

AN:

151944

Hom.:

1115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.189

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.0794

Gnomad ASJ

AF:

0.0618

Gnomad EAS

AF:

0.0859

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.0596

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0818

Gnomad OTH

AF:

0.107

GnomAD4 exome

AF:

0.0851

AC:

69020

AN:

810806

Hom.:

3563

AF XY:

0.0882

AC XY:

37758

AN XY:

428134

show subpopulations

Gnomad4 AFR exome

AF:

0.185

Gnomad4 AMR exome

AF:

0.0456

Gnomad4 ASJ exome

AF:

0.0686

Gnomad4 EAS exome

AF:

0.0640

Gnomad4 SAS exome

AF:

0.147

Gnomad4 FIN exome

AF:

0.0611

Gnomad4 NFE exome

AF:

0.0796

Gnomad4 OTH exome

AF:

0.0921

GnomAD4 genome

AF:

0.112

AC:

16973

AN:

152062

Hom.:

1115

Cov.:

AF XY:

0.112

AC XY:

8345

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.189

Gnomad4 AMR

AF:

0.0794

Gnomad4 ASJ

AF:

0.0618

Gnomad4 EAS

AF:

0.0854

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.0596

Gnomad4 NFE

AF:

0.0818

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.101

Hom.:

151

Bravo

AF:

0.113

Asia WGS

AF:

0.136

AC:

472

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2019	This variant is associated with the following publications: (PMID: 18852354) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.71

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