rs3755557

Variant names:

• chr3-120096110-T-A
• rs3755557
• ENST00000484076.1:n.193T>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.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
• Publications: 49 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	NR_186627.1		n.675+332T>A		intron	N/A
	GSK3B-DT	NR_186628.1		n.675+332T>A		intron	N/A
	GSK3B-DT	NR_186629.1		n.675+332T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	ENST00000484076.1	TSL:1	n.193T>A		non_coding_transcript_exon	Exon 2 of 6
	GSK3B-DT	ENST00000686307.3		n.879T>A		non_coding_transcript_exon	Exon 1 of 3
	GSK3B-DT	ENST00000834995.1		n.79T>A		non_coding_transcript_exon	Exon 1 of 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

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: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 2 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.114 AC: 4730 AN: 41516

American (AMR) AF: 0.151 AC: 2313 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3468

East Asian (EAS) AF: 0.141 AC: 730 AN: 5176

South Asian (SAS) AF: 0.184 AC: 887 AN: 4824

European-Finnish (FIN) AF: 0.180 AC: 1902 AN: 10586

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9683 AN: 67994

Other (OTH) AF: 0.159 AC: 336 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.2
DANN	Benign	0.61
PhyloP100		-0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3755557;

hg19: chr3-119814957;