Genetic Variant UGGT1:n.*4897G>A (chr2-128189931-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000376723.7(UGGT1):n.*4897G>A variant causes a non coding transcript exon 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
ENST00000376723.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.99

Publications

12 publications found

Variant links:

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

UGGT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGGT1	NM_020120.4 link	c.*189G>A		3_prime_UTR_variant	Exon 41 of 41	ENST00000259253.11	NP_064505.1	Q9NYU2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGGT1	ENST00000259253.11 link	c.*189G>A		3_prime_UTR_variant	Exon 41 of 41	1	NM_020120.4	ENSP00000259253.6		Q9NYU2-1

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64504

AN:

151902

Hom.:

13906

Cov.:

show subpopulations

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.:

AF XY:

0.438

AC XY:

98830

AN XY:

225424

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

4809

9618

14426

19235

24044

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1170

2340

3510

4680

5850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.425

AC:

64557

AN:

152020

Hom.:

13913

Cov.:

AF XY:

0.427

AC XY:

31743

AN XY:

74294

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1894

3788

5682

7576

9470

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

612

1224

1836

2448

3060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.0030

(source)

DANN

Benign

0.37

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over