rs2290110

chr2-128178426-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020120.4(UGGT1):c.3714-42T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 1,506,652 control chromosomes in the GnomAD database, including 144,419 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: 0.44 (130506 hom.)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.89).
• 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.3714-42T>C		intron_variant		ENST00000259253.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGGT1	ENST00000259253.11	c.3714-42T>C		intron_variant		1	NM_020120.4	P1
UGGT1	ENST00000376723.7	c.*3754-42T>C		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64499 AN: 151866 Hom.: 13906 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.397

GnomAD3 exomes AF: 0.437 AC: 98015 AN: 224438 Hom.: 22095 AF XY: 0.442 AC XY: 53848 AN XY: 121696

Gnomad AFR exome AF: 0.422

Gnomad AMR exome AF: 0.375

Gnomad ASJ exome AF: 0.421

Gnomad EAS exome AF: 0.338

Gnomad SAS exome AF: 0.569

Gnomad FIN exome AF: 0.491

Gnomad NFE exome AF: 0.430

Gnomad OTH exome AF: 0.440

GnomAD4 exome AF: 0.435 AC: 589777 AN: 1354668 Hom.: 130506 Cov.: 19 AF XY: 0.439 AC XY: 297482 AN XY: 677808

Gnomad4 AFR exome AF: 0.419

Gnomad4 AMR exome AF: 0.373

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.349

Gnomad4 SAS exome AF: 0.566

Gnomad4 FIN exome AF: 0.491

Gnomad4 NFE exome AF: 0.429

Gnomad4 OTH exome AF: 0.433

GnomAD4 genome AF: 0.425 AC: 64552 AN: 151984 Hom.: 13913 Cov.: 32 AF XY: 0.427 AC XY: 31744 AN XY: 74282

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.403

Alfa AF: 0.422 Hom.: 3078

Bravo AF: 0.412

Asia WGS AF: 0.512 AC: 1783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.34

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: rs2290110; hg19: chr2-128936000; COSMIC: COSV52141328; COSMIC: COSV52141328;