Variant chr3-120098826-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000484076.1(GSK3B-DT):n.345+34A>T 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 0.0627 in 152,284 control chromosomes in the GnomAD database, including 426 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 0.063 ( 425 hom., cov: 32)

Exomes 𝑓: 0.13 ( 1 hom. )

Consequence

GSK3B-DT
ENST00000484076.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0860

Variant links:

Genes affected

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

GSK3B-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
GSK3B-DT	ENST00000484076.1 linkuse as main transcript	n.345+34A>T	intron_variant, non_coding_transcript_variant		1
GSK3B-DT	ENST00000469070.1 linkuse as main transcript	n.622A>T	non_coding_transcript_exon_variant	2/2	3
GSK3B-DT	ENST00000485898.2 linkuse as main transcript	n.584A>T	non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.0627

AC:

9543

AN:

152150

Hom.:

426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0173

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.0725

Gnomad ASJ

AF:

0.102

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0143

Gnomad FIN

AF:

0.0774

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0895

Gnomad OTH

AF:

0.0840

GnomAD4 exome

AF:

0.125

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0626

AC:

9539

AN:

152268

Hom.:

425

Cov.:

AF XY:

0.0609

AC XY:

4535

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0172

Gnomad4 AMR

AF:

0.0723

Gnomad4 ASJ

AF:

0.102

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0141

Gnomad4 FIN

AF:

0.0774

Gnomad4 NFE

AF:

0.0895

Gnomad4 OTH

AF:

0.0832

Alfa

AF:

0.0689

Hom.:

Bravo

AF:

0.0619

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.5

DANN

Benign

0.47

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over