3-120105190-G-A

Position:

• chr3-120105190-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+345G>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 0.0672 in 152,262 control chromosomes in the GnomAD database, including 380 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 0.067 (380 hom., cov: 32)
• Consequence: GSK3B-DT ENST00000484076.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.083 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSK3B-DT	ENST00000484076.1	n.415+345G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 10236 AN: 152144 Hom.: 380 Cov.: 32

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0672 AC: 10235 AN: 152262 Hom.: 380 Cov.: 32 AF XY: 0.0641 AC XY: 4775 AN XY: 74450

Gnomad4 AFR AF: 0.0531

Gnomad4 AMR AF: 0.0642

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0388

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0848

Gnomad4 OTH AF: 0.0810

Alfa AF: 0.0819 Hom.: 784

Bravo AF: 0.0688

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11927974; hg19: chr3-119824037;