chr2-128093088-C-A

Variant names:

• chr2-128093088-C-A
• rs11687190
• NM_020120.4:c.58+1673C>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.58+1673C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,988 control chromosomes in the GnomAD database, including 25,657 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 0.58 (25657 hom., cov: 32)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGGT1	NM_020120.4	c.58+1673C>A		intron_variant	Intron 1 of 40	ENST00000259253.11	NP_064505.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGGT1	ENST00000259253.11	c.58+1673C>A		intron_variant	Intron 1 of 40	1	NM_020120.4	ENSP00000259253.6
UGGT1	ENST00000376723.7	n.*98+1492C>A		intron_variant	Intron 1 of 40	1		ENSP00000365913.3
UGGT1	ENST00000438277.5	n.25+1706C>A		intron_variant	Intron 1 of 25	1		ENSP00000392701.1
UGGT1	ENST00000430075.5	n.25+1706C>A		intron_variant	Intron 1 of 4	4		ENSP00000400426.1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87869 AN: 151872 Hom.: 25650 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.579 AC: 87927 AN: 151988 Hom.: 25657 Cov.: 32 AF XY: 0.576 AC XY: 42790 AN XY: 74276

African (AFR) AF: 0.593 AC: 24552 AN: 41434

American (AMR) AF: 0.646 AC: 9871 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1978 AN: 3468

East Asian (EAS) AF: 0.660 AC: 3408 AN: 5162

South Asian (SAS) AF: 0.426 AC: 2050 AN: 4814

European-Finnish (FIN) AF: 0.507 AC: 5357 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.571 AC: 38797 AN: 67970

Other (OTH) AF: 0.600 AC: 1265 AN: 2108

Alfa AF: 0.557 Hom.: 13767

Bravo AF: 0.593

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.2
DANN	Benign	0.59
PhyloP100		0.29
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: rs11687190; hg19: chr2-128850662;