chr2-128151912-C-T

Variant names:

• chr2-128151912-C-T
• rs12471108
• NM_020120.4:c.2017-872C>T

Variant summary

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

The NM_020120.4(UGGT1):​c.2017-872C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,044 control chromosomes in the GnomAD database, including 26,795 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 0.59 (26795 hom., cov: 32)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020120.4. 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
	UGGT1	NM_020120.4	MANE Select	c.2017-872C>T		intron	N/A	NP_064505.1	Q9NYU2-1
	UGGT1	NR_027671.3		n.2356-872C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGGT1	ENST00000259253.11	TSL:1 MANE Select	c.2017-872C>T		intron	N/A	ENSP00000259253.6	Q9NYU2-1
	UGGT1	ENST00000376723.7	TSL:1	n.*2057-872C>T		intron	N/A	ENSP00000365913.3	E2QRN8
	UGGT1	ENST00000438277.5	TSL:1	n.*1605-872C>T		intron	N/A	ENSP00000392701.1	F8WCI2

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89751 AN: 151924 Hom.: 26775 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.591 AC: 89825 AN: 152044 Hom.: 26795 Cov.: 32 AF XY: 0.588 AC XY: 43695 AN XY: 74326

African (AFR) AF: 0.634 AC: 26268 AN: 41458

American (AMR) AF: 0.653 AC: 9969 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1980 AN: 3472

East Asian (EAS) AF: 0.661 AC: 3421 AN: 5178

South Asian (SAS) AF: 0.428 AC: 2061 AN: 4820

European-Finnish (FIN) AF: 0.507 AC: 5359 AN: 10566

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38826 AN: 67962

Other (OTH) AF: 0.611 AC: 1289 AN: 2110

Alfa AF: 0.506 Hom.: 2076

Bravo AF: 0.606

Asia WGS AF: 0.493 AC: 1711 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	0.66
DANN	Benign	0.20
PhyloP100		-0.62
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: rs12471108; hg19: chr2-128909486;