3-119931941-T-C

Variant names:

• chr3-119931941-T-C
• rs9878473
• NM_001146156.2:c.367-8458A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001146156.2(GSK3B):​c.367-8458A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,010 control chromosomes in the GnomAD database, including 25,147 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 0.54 (25147 hom., cov: 32)
• Consequence: GSK3B NM_001146156.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 8 publications found

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 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics

ENSG00000297780 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001146156.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B	NM_001146156.2	MANE Select	c.367-8458A>G		intron	N/A	NP_001139628.1	Q6FI27
	GSK3B	NM_002093.4		c.367-8458A>G		intron	N/A	NP_002084.2
	GSK3B	NM_001354596.2		c.367-8458A>G		intron	N/A	NP_001341525.1	A0A3B3ITW1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B	ENST00000264235.13	TSL:1 MANE Select	c.367-8458A>G		intron	N/A	ENSP00000264235.9	P49841-1
	GSK3B	ENST00000316626.6	TSL:1	c.367-8458A>G		intron	N/A	ENSP00000324806.5	P49841-2
	GSK3B	ENST00000678439.1		c.367-8458A>G		intron	N/A	ENSP00000503868.1	A0A7I2YQK0

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81293 AN: 151892 Hom.: 25084 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.536 AC: 81417 AN: 152010 Hom.: 25147 Cov.: 32 AF XY: 0.533 AC XY: 39583 AN XY: 74314

African (AFR) AF: 0.864 AC: 35863 AN: 41488

American (AMR) AF: 0.416 AC: 6352 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1448 AN: 3466

East Asian (EAS) AF: 0.585 AC: 3025 AN: 5170

South Asian (SAS) AF: 0.499 AC: 2404 AN: 4820

European-Finnish (FIN) AF: 0.382 AC: 4025 AN: 10530

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26776 AN: 67952

Other (OTH) AF: 0.516 AC: 1084 AN: 2100

Alfa AF: 0.419 Hom.: 2751

Bravo AF: 0.548

Asia WGS AF: 0.567 AC: 1966 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.96
DANN	Benign	0.68
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9878473; hg19: chr3-119650788;