rs3738923

Variant names:

• chr2-128156183-G-A
• rs3738923
• NM_020120.4:c.2237-209G>A

Variant summary

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

The NM_020120.4(UGGT1):​c.2237-209G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,962 control chromosomes in the GnomAD database, including 24,984 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 0.57 (24984 hom., cov: 31)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934
• Publications: 6 publications found

Genes affected

UGGT1 (HGNC:15663): (UDP-glucose glycoprotein glucosyltransferase 1) UDP-glucose:glycoprotein glucosyltransferase (UGT) is a soluble protein of the endoplasmic reticulum (ER) that selectively reglucosylates unfolded glycoproteins, thus providing quality control for protein transport out of the ER.[supplied by OMIM, Oct 2009]

UGGT1 Gene-Disease associations (from GenCC):

• disorder of protein N-glycosylation

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGGT1	NM_020120.4	c.2237-209G>A		intron_variant	Intron 20 of 40	ENST00000259253.11	NP_064505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGGT1	ENST00000259253.11	c.2237-209G>A		intron_variant	Intron 20 of 40	1	NM_020120.4	ENSP00000259253.6
UGGT1	ENST00000376723.7	n.*2277-209G>A		intron_variant	Intron 20 of 40	1		ENSP00000365913.3
UGGT1	ENST00000438277.5	n.*1825-209G>A		intron_variant	Intron 18 of 25	1		ENSP00000392701.1
UGGT1	ENST00000488439.1	n.536+596G>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86500 AN: 151844 Hom.: 24961 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.539

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.570 AC: 86573 AN: 151962 Hom.: 24984 Cov.: 31 AF XY: 0.568 AC XY: 42233 AN XY: 74290

African (AFR) AF: 0.571 AC: 23640 AN: 41418

American (AMR) AF: 0.474 AC: 7226 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3472

East Asian (EAS) AF: 0.350 AC: 1805 AN: 5158

South Asian (SAS) AF: 0.652 AC: 3142 AN: 4822

European-Finnish (FIN) AF: 0.617 AC: 6525 AN: 10570

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40438 AN: 67956

Other (OTH) AF: 0.544 AC: 1147 AN: 2108

Alfa AF: 0.586 Hom.: 3949

Bravo AF: 0.554

Asia WGS AF: 0.583 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.046
DANN	Benign	0.57
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3738923; hg19: chr2-128913757;