Genetic Variant 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

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 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=-0.89).

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 rank	MANE	Protein	UniProt
UGGT1	NM_020120.4 link	c.3714-42T>C		intron_variant	Intron 33 of 40	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.3714-42T>C		intron_variant	Intron 33 of 40	1	NM_020120.4	ENSP00000259253.6		Q9NYU2-1
UGGT1	ENST00000376723.7 link	n.*3754-42T>C		intron_variant	Intron 33 of 40	1		ENSP00000365913.3		E2QRN8

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

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

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 v4.3

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

Publications

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2-128178426-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

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