rs334538

chr3-120106364-G-A

Variant summary

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

The ENST00000484076.1(GSK3B-DT):n.415+1519G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSK3B-DT	ENST00000484076.1	n.415+1519G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.0829

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.206

Alfa AF: 0.189 Hom.: 781

Bravo AF: 0.202

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.41
Dann	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs334538; hg19: chr3-119825211;