rs11542865

chr2-128189931-G-Achr2-128189931-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGGT1	NM_020120.4	c.*189G>A		3_prime_UTR_variant	41/41	ENST00000259253.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGGT1	ENST00000259253.11	c.*189G>A		3_prime_UTR_variant	41/41	1	NM_020120.4	P1
UGGT1	ENST00000376723.7	c.*4897G>A		3_prime_UTR_variant, NMD_transcript_variant	41/41	1
UGGT1	ENST00000418197.1	c.*189G>A		3_prime_UTR_variant	4/4	5
UGGT1	ENST00000465836.1	n.464G>A		non_coding_transcript_exon_variant	3/3	2

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

Gnomad4 AFR exome AF: 0.419

Gnomad4 AMR exome AF: 0.365

Gnomad4 ASJ exome AF: 0.414

Gnomad4 EAS exome AF: 0.351

Gnomad4 SAS exome AF: 0.568

Gnomad4 FIN exome AF: 0.496

Gnomad4 NFE exome AF: 0.426

Gnomad4 OTH exome AF: 0.431

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

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.404

Alfa AF: 0.414 Hom.: 13513

Bravo AF: 0.412

Asia WGS AF: 0.513 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.0030
Dann	Benign	0.37

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

Publications

LitVar

Other links and lift over

dbSNP: rs11542865; hg19: chr2-128947505; COSMIC: COSV52135074;