ENST00000484076.1:n.415+2472A>T

Variant names:

• chr3-120107317-A-T
• rs12053912
• ENST00000484076.1:n.415+2472A>T

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+2472A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,194 control chromosomes in the GnomAD database, including 3,958 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 0.21 (3958 hom., cov: 33)
• Consequence: GSK3B-DT ENST00000484076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSK3B-DT	NR_186627.1	n.676-857A>T		intron_variant	Intron 1 of 1
GSK3B-DT	NR_186628.1	n.942-857A>T		intron_variant	Intron 2 of 2
GSK3B-DT	NR_186629.1	n.746-857A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSK3B-DT	ENST00000484076.1	n.415+2472A>T		intron_variant	Intron 4 of 5	1
GSK3B-DT	ENST00000834988.1	n.309+8338A>T		intron_variant	Intron 2 of 3
GSK3B-DT	ENST00000834989.1	n.482+11539A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31672 AN: 152074 Hom.: 3951 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.208 AC: 31712 AN: 152194 Hom.: 3958 Cov.: 33 AF XY: 0.214 AC XY: 15922 AN XY: 74396

African (AFR) AF: 0.242 AC: 10034 AN: 41530

American (AMR) AF: 0.143 AC: 2181 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2899 AN: 5160

South Asian (SAS) AF: 0.302 AC: 1459 AN: 4826

European-Finnish (FIN) AF: 0.267 AC: 2820 AN: 10578

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.164 AC: 11124 AN: 68020

Other (OTH) AF: 0.191 AC: 404 AN: 2112

Alfa AF: 0.196 Hom.: 397

Bravo AF: 0.199

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12053912; hg19: chr3-119826164;