dbSNP rs2290110: UGGT1:c.3714-42T>C (chr2-128178426-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.30

Publications

6 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

new If you want to explore the variant's impact on the transcript NM_020120.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.89).

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.3714-42T>C		intron	N/A	NP_064505.1	Q9NYU2-1
	UGGT1	NR_027671.3		n.4053-42T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UGGT1	ENST00000259253.11	TSL:1 MANE Select	c.3714-42T>C	intron	N/A	ENSP00000259253.6	Q9NYU2-1
UGGT1	ENST00000376723.7	TSL:1	n.*3754-42T>C	intron	N/A	ENSP00000365913.3	E2QRN8
UGGT1	ENST00000933134.1		c.3711-42T>C	intron	N/A	ENSP00000603193.1

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64499

AN:

151866

Hom.:

13906

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.437

AC:

98015

AN:

224438

AF XY:

0.442

show subpopulations

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 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.:

AF XY:

0.439

AC XY:

297482

AN XY:

677808

show subpopulations

African (AFR)

AF:

0.419

AC:

12599

AN:

30104

American (AMR)

AF:

0.373

AC:

13993

AN:

37518

Ashkenazi Jewish (ASJ)

AF:

0.418

AC:

10031

AN:

23992

East Asian (EAS)

AF:

0.349

AC:

13559

AN:

38900

South Asian (SAS)

AF:

0.566

AC:

44817

AN:

79124

European-Finnish (FIN)

AF:

0.491

AC:

25751

AN:

52426

Middle Eastern (MID)

AF:

0.376

AC:

2015

AN:

5362

European-Non Finnish (NFE)

AF:

0.429

AC:

442549

AN:

1030776

Other (OTH)

AF:

0.433

AC:

24463

AN:

56466

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

15962

31924

47885

63847

79809

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13256

26512

39768

53024

66280

<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:

64552

AN:

151984

Hom.:

13913

Cov.:

AF XY:

0.427

AC XY:

31744

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.417

AC:

17264

AN:

41416

American (AMR)

AF:

0.360

AC:

5496

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1489

AN:

3468

East Asian (EAS)

AF:

0.339

AC:

1758

AN:

5182

South Asian (SAS)

AF:

0.573

AC:

2753

AN:

4806

European-Finnish (FIN)

AF:

0.492

AC:

5190

AN:

10548

Middle Eastern (MID)

AF:

0.397

AC:

116

AN:

292

European-Non Finnish (NFE)

AF:

0.430

AC:

29195

AN:

67972

Other (OTH)

AF:

0.403

AC:

853

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1904

3809

5713

7618

9522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<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.:

3143

Bravo

AF:

0.412

Asia WGS

AF:

0.512

AC:

1783

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.9

(source)

DANN

Benign

0.34

PhyloP100

-1.3

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over