chr3-120106364-G-A

Variant names:

• chr3-120106364-G-A
• rs334538
• ENST00000484076.1:n.415+1519G>A

Variant summary

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

The ENST00000484076.1(GSK3B-DT):​n.415+1519G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,106 control chromosomes in the GnomAD database, including 3,253 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 0.20 (3253 hom., cov: 32)
• Consequence: GSK3B-DT ENST00000484076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 7 publications found

Genes affected

GSK3B-DT (HGNC:55635): (GSK3B divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484076.1. 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-DT	NR_186627.1		n.676-1810G>A		intron	N/A
	GSK3B-DT	NR_186628.1		n.942-1810G>A		intron	N/A
	GSK3B-DT	NR_186629.1		n.745+1519G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	ENST00000484076.1	TSL:1	n.415+1519G>A		intron	N/A
	GSK3B-DT	ENST00000834988.1		n.309+7385G>A		intron	N/A
	GSK3B-DT	ENST00000834989.1		n.482+10586G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30188 AN: 151988 Hom.: 3244 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.199 AC: 30225 AN: 152106 Hom.: 3253 Cov.: 32 AF XY: 0.196 AC XY: 14552 AN XY: 74352

African (AFR) AF: 0.277 AC: 11477 AN: 41464

American (AMR) AF: 0.148 AC: 2264 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3468

East Asian (EAS) AF: 0.0829 AC: 429 AN: 5174

South Asian (SAS) AF: 0.226 AC: 1086 AN: 4814

European-Finnish (FIN) AF: 0.107 AC: 1130 AN: 10590

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12466 AN: 67994

Other (OTH) AF: 0.206 AC: 435 AN: 2114

Alfa AF: 0.190 Hom.: 803

Bravo AF: 0.202

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
DANN	Benign	0.13
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs334538; hg19: chr3-119825211;