rs17471

Variant names:

• chr3-120098826-A-T
• rs17471
• ENST00000484076.1:n.345+34A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484076.1(GSK3B-DT):​n.345+34A>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484076.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	NR_186628.1		n.788A>T		non_coding_transcript_exon	Exon 2 of 3
	GSK3B-DT	NR_186632.1		n.788A>T		non_coding_transcript_exon	Exon 2 of 3
	GSK3B-DT	NR_186633.1		n.788A>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	ENST00000484076.1	TSL:1	n.345+34A>T		intron	N/A
	GSK3B-DT	ENST00000469070.2	TSL:3	n.1155A>T		non_coding_transcript_exon	Exon 2 of 2
	GSK3B-DT	ENST00000485898.2	TSL:3	n.584A>T		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 2 AN: 12

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0626 AC: 9539 AN: 152268 Hom.: 425 Cov.: 32 AF XY: 0.0609 AC XY: 4535 AN XY: 74454

African (AFR) AF: 0.0172 AC: 715 AN: 41554

American (AMR) AF: 0.0723 AC: 1106 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4826

European-Finnish (FIN) AF: 0.0774 AC: 821 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0895 AC: 6086 AN: 68004

Other (OTH) AF: 0.0832 AC: 176 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs17471; hg19: chr3-119817673;