rs3755557

chr3-120096110-T-A

Variant summary

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

The ENST00000484076.1(GSK3B-DT):n.193T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,220 control chromosomes in the GnomAD database, including 1,574 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 0.14 (1574 hom., cov: 33)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: GSK3B-DT ENST00000484076.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 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.193T>A		non_coding_transcript_exon_variant	2/6	1
GSK3B-DT	ENST00000686307.2	n.879T>A		non_coding_transcript_exon_variant	1/1
GSK3B-DT	ENST00000469070.1	n.509+332T>A		intron_variant, non_coding_transcript_variant		3
GSK3B-DT	ENST00000485898.2	n.149+332T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21269 AN: 152076 Hom.: 1566 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.115 AC: 3 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.0909 AC XY: 2 AN XY: 22

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.140 AC: 21295 AN: 152194 Hom.: 1574 Cov.: 33 AF XY: 0.142 AC XY: 10570 AN XY: 74406

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.159

Alfa AF: 0.143 Hom.: 187

Bravo AF: 0.138

Asia WGS AF: 0.180 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	3.2
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3755557; hg19: chr3-119814957;