3-120098139-G-C

Position:

• chr3-120098139-G-C

Variant summary

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

The ENST00000484076.1(GSK3B-DT):​n.267-575G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,156 control chromosomes in the GnomAD database, including 599 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 0.084 (599 hom., cov: 33)
• Consequence: GSK3B-DT ENST00000484076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

GSK3B-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSK3B-DT	NR_186627.1	n.675+2361G>C		intron_variant
GSK3B-DT	NR_186628.1	n.676-575G>C		intron_variant
GSK3B-DT	NR_186629.1	n.675+2361G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSK3B-DT	ENST00000484076.1	n.267-575G>C		intron_variant		1
GSK3B-DT	ENST00000469070.1	n.510-575G>C		intron_variant		3
GSK3B-DT	ENST00000485898.2	n.150-253G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0842 AC: 12794 AN: 152038 Hom.: 599 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0841 AC: 12800 AN: 152156 Hom.: 599 Cov.: 33 AF XY: 0.0806 AC XY: 5994 AN XY: 74390

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0831

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0406

Gnomad4 FIN AF: 0.0398

Gnomad4 NFE AF: 0.0865

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0250 Hom.: 12

Bravo AF: 0.0896

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17811013; hg19: chr3-119816986;