dbSNP rs7986005: UGGT2:c.1677+20G>A (chr13-95947017-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020121.4(UGGT2):c.1677+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,534,632 control chromosomes in the GnomAD database, including 126,929 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 0.40 ( 12266 hom., cov: 33)

Exomes 𝑓: 0.40 ( 114663 hom. )

Consequence

UGGT2
NM_020121.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.21

Publications

7 publications found

Variant links:

Genes affected

UGGT2 (HGNC:15664): (UDP-glucose glycoprotein glucosyltransferase 2) 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]

UGGT2 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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020121.4. 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
	UGGT2	NM_020121.4	MANE Select	c.1677+20G>A		intron	N/A	NP_064506.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UGGT2	ENST00000376747.8	TSL:1 MANE Select	c.1677+20G>A	intron	N/A	ENSP00000365938.3	Q9NYU1-1
UGGT2	ENST00000943424.1		c.1677+20G>A	intron	N/A	ENSP00000613483.1
UGGT2	ENST00000943423.1		c.1677+20G>A	intron	N/A	ENSP00000613482.1

Frequencies

GnomAD3 genomes

AF:

0.399

AC:

60574

AN:

151866

Hom.:

12269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.406

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.437

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.390

GnomAD2 exomes

AF:

0.383

AC:

77765

AN:

202918

AF XY:

0.388

show subpopulations

Gnomad AFR exome

AF:

0.398

Gnomad AMR exome

AF:

0.210

Gnomad ASJ exome

AF:

0.418

Gnomad EAS exome

AF:

0.311

Gnomad FIN exome

AF:

0.438

Gnomad NFE exome

AF:

0.419

Gnomad OTH exome

AF:

0.402

GnomAD4 exome

AF:

0.405

AC:

559502

AN:

1382648

Hom.:

114663

Cov.:

AF XY:

0.405

AC XY:

276725

AN XY:

683522

show subpopulations

African (AFR)

AF:

0.405

AC:

12280

AN:

30316

American (AMR)

AF:

0.224

AC:

6516

AN:

29136

Ashkenazi Jewish (ASJ)

AF:

0.421

AC:

9629

AN:

22860

East Asian (EAS)

AF:

0.316

AC:

12122

AN:

38396

South Asian (SAS)

AF:

0.362

AC:

26836

AN:

74122

European-Finnish (FIN)

AF:

0.441

AC:

22691

AN:

51418

Middle Eastern (MID)

AF:

0.444

AC:

2360

AN:

5310

European-Non Finnish (NFE)

AF:

0.413

AC:

443910

AN:

1074318

Other (OTH)

AF:

0.408

AC:

23158

AN:

56772

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

14499

28998

43496

57995

72494

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13852

27704

41556

55408

69260

<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:

0.399

AC:

60598

AN:

151984

Hom.:

12266

Cov.:

AF XY:

0.398

AC XY:

29533

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.405

AC:

16802

AN:

41440

American (AMR)

AF:

0.319

AC:

4870

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.431

AC:

1494

AN:

3470

East Asian (EAS)

AF:

0.323

AC:

1667

AN:

5168

South Asian (SAS)

AF:

0.352

AC:

1695

AN:

4814

European-Finnish (FIN)

AF:

0.437

AC:

4607

AN:

10546

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.415

AC:

28187

AN:

67960

Other (OTH)

AF:

0.390

AC:

822

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1864

3728

5591

7455

9319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<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:

0.400

Hom.:

2693

Bravo

AF:

0.384

Asia WGS

AF:

0.336

AC:

1170

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.5

(source)

DANN

Benign

0.51

PhyloP100

2.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over