3-120098826-A-T

Position:

• chr3-120098826-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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=-0.84).
• 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	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSK3B-DT	ENST00000484076.1	n.345+34A>T		intron_variant, non_coding_transcript_variant		1
GSK3B-DT	ENST00000469070.1	n.622A>T		non_coding_transcript_exon_variant	2/2	3
GSK3B-DT	ENST00000485898.2	n.584A>T		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9543 AN: 152150 Hom.: 426 Cov.: 32

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: 2 AN: 16 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

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.: 32 AF XY: 0.0609 AC XY: 4535 AN XY: 74454

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.: 49

Bravo AF: 0.0619

Asia WGS AF: 0.0160 AC: 57 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

Other links and lift over

dbSNP: rs17471; hg19: chr3-119817673;