rs744265

chr2-128186850-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.4476+51T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 1,248,680 control chromosomes in the GnomAD database, including 217,164 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 0.57 (25237 hom., cov: 30)
  • Exomes 𝑓: 0.59 (191927 hom.)
• Consequence: UGGT1 NM_020120.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UGGT1	NM_020120.4	c.4476+51T>C		intron_variant		ENST00000259253.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGGT1	ENST00000259253.11	c.4476+51T>C		intron_variant		1	NM_020120.4	P1
UGGT1	ENST00000376723.7	c.*4516+51T>C		intron_variant, NMD_transcript_variant		1
UGGT1	ENST00000418197.1	c.202+51T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86853 AN: 151536 Hom.: 25215 Cov.: 30

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.542

GnomAD3 exomes AF: 0.567 AC: 114193 AN: 201332 Hom.: 33308 AF XY: 0.573 AC XY: 63203 AN XY: 110284

Gnomad AFR exome AF: 0.584

Gnomad AMR exome AF: 0.457

Gnomad ASJ exome AF: 0.558

Gnomad EAS exome AF: 0.341

Gnomad SAS exome AF: 0.645

Gnomad FIN exome AF: 0.616

Gnomad NFE exome AF: 0.594

Gnomad OTH exome AF: 0.576

GnomAD4 exome AF: 0.587 AC: 644429 AN: 1097026 Hom.: 191927 Cov.: 13 AF XY: 0.589 AC XY: 325890 AN XY: 553632

Gnomad4 AFR exome AF: 0.585

Gnomad4 AMR exome AF: 0.457

Gnomad4 ASJ exome AF: 0.557

Gnomad4 EAS exome AF: 0.359

Gnomad4 SAS exome AF: 0.642

Gnomad4 FIN exome AF: 0.620

Gnomad4 NFE exome AF: 0.598

Gnomad4 OTH exome AF: 0.578

GnomAD4 genome AF: 0.573 AC: 86926 AN: 151654 Hom.: 25237 Cov.: 30 AF XY: 0.572 AC XY: 42378 AN XY: 74106

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.547

Alfa AF: 0.574 Hom.: 33203

Bravo AF: 0.559

Asia WGS AF: 0.582 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.5
Dann	Benign	0.31

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: rs744265; hg19: chr2-128944424; COSMIC: COSV52141334; COSMIC: COSV52141334;