rs11542865

Variant names:

• chr2-128189931-G-A
• rs11542865
• NM_020120.4:c.*189G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-128189931-G-A
• chr2-128189931-G-C

Variant summary

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

The NM_020120.4(UGGT1):​c.*189G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 583,126 control chromosomes in the GnomAD database, including 55,556 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 0.42 (13913 hom., cov: 32)
  • Exomes 𝑓: 0.43 (41643 hom.)
• Consequence: UGGT1 NM_020120.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 12 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.555 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.*189G>A		3_prime_UTR	Exon 41 of 41	NP_064505.1	Q9NYU2-1
	UGGT1	NR_027671.3		n.5196G>A		non_coding_transcript_exon	Exon 41 of 41

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGGT1	ENST00000259253.11	TSL:1 MANE Select	c.*189G>A		3_prime_UTR	Exon 41 of 41	ENSP00000259253.6	Q9NYU2-1
	UGGT1	ENST00000376723.7	TSL:1	n.*4897G>A		non_coding_transcript_exon	Exon 41 of 41	ENSP00000365913.3	E2QRN8
	UGGT1	ENST00000376723.7	TSL:1	n.*4897G>A		3_prime_UTR	Exon 41 of 41	ENSP00000365913.3	E2QRN8

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64504 AN: 151902 Hom.: 13906 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.398

GnomAD4 exome AF: 0.433 AC: 186697 AN: 431106 Hom.: 41643 Cov.: 6 AF XY: 0.438 AC XY: 98830 AN XY: 225424

African (AFR) AF: 0.419 AC: 5228 AN: 12480

American (AMR) AF: 0.365 AC: 6928 AN: 18964

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 5204 AN: 12566

East Asian (EAS) AF: 0.351 AC: 10536 AN: 30052

South Asian (SAS) AF: 0.568 AC: 19359 AN: 34088

European-Finnish (FIN) AF: 0.496 AC: 13742 AN: 27706

Middle Eastern (MID) AF: 0.381 AC: 1137 AN: 2986

European-Non Finnish (NFE) AF: 0.426 AC: 114150 AN: 268108

Other (OTH) AF: 0.431 AC: 10413 AN: 24156

GnomAD4 genome AF: 0.425 AC: 64557 AN: 152020 Hom.: 13913 Cov.: 32 AF XY: 0.427 AC XY: 31743 AN XY: 74294

African (AFR) AF: 0.417 AC: 17272 AN: 41464

American (AMR) AF: 0.360 AC: 5493 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1754 AN: 5166

South Asian (SAS) AF: 0.573 AC: 2759 AN: 4814

European-Finnish (FIN) AF: 0.492 AC: 5201 AN: 10570

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29178 AN: 67944

Other (OTH) AF: 0.404 AC: 854 AN: 2114

Alfa AF: 0.422 Hom.: 36362

Bravo AF: 0.412

Asia WGS AF: 0.513 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0030
DANN	Benign	0.37
PhyloP100		-2.0
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: rs11542865; hg19: chr2-128947505; COSMIC: COSV52135074;