chr3-120105190-G-A

Variant names:

• chr3-120105190-G-A
• rs11927974
• ENST00000484076.1:n.415+345G>A

Variant summary

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

The ENST00000484076.1(GSK3B-DT):​n.415+345G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 13 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.083 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_186630.1		n.1169G>A		non_coding_transcript_exon	Exon 3 of 3
	GSK3B-DT	NR_186627.1		n.676-2984G>A		intron	N/A
	GSK3B-DT	NR_186628.1		n.942-2984G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	ENST00000484076.1	TSL:1	n.415+345G>A		intron	N/A
	GSK3B-DT	ENST00000834992.1		n.1214G>A		non_coding_transcript_exon	Exon 2 of 2
	GSK3B-DT	ENST00000834993.1		n.1169G>A		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.0531 AC: 2206 AN: 41554

American (AMR) AF: 0.0642 AC: 982 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0388 AC: 187 AN: 4814

European-Finnish (FIN) AF: 0.0416 AC: 441 AN: 10612

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0848 AC: 5769 AN: 68004

Other (OTH) AF: 0.0810 AC: 171 AN: 2112

Alfa AF: 0.0789 Hom.: 1073

Bravo AF: 0.0688

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.38
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11927974; hg19: chr3-119824037;