Genetic Variant NM_020120.4:c.*579T>C (chr2-128190321-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.*579T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,114 control chromosomes in the GnomAD database, including 14,151 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 0.43 ( 14132 hom., cov: 31)

Exomes 𝑓: 0.44 ( 19 hom. )

Consequence

UGGT1
NM_020120.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

8 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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.*579T>C		3_prime_UTR	Exon 41 of 41	NP_064505.1	Q9NYU2-1
	UGGT1	NR_027671.3		n.5586T>C		non_coding_transcript_exon	Exon 41 of 41

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UGGT1	ENST00000259253.11	TSL:1 MANE Select	c.*579T>C	3_prime_UTR	Exon 41 of 41	ENSP00000259253.6	Q9NYU2-1
UGGT1	ENST00000376723.7	TSL:1	n.*5287T>C	non_coding_transcript_exon	Exon 41 of 41	ENSP00000365913.3	E2QRN8
UGGT1	ENST00000376723.7	TSL:1	n.*5287T>C	3_prime_UTR	Exon 41 of 41	ENSP00000365913.3	E2QRN8

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

64963

AN:

151770

Hom.:

14125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.428

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.360

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.573

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.398

GnomAD4 exome

AF:

0.442

AC:

100

AN:

226

Hom.:

Cov.:

AF XY:

0.410

AC XY:

AN XY:

134

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.286

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.450

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.466

AC:

AN:

178

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.428

AC:

65016

AN:

151888

Hom.:

14132

Cov.:

AF XY:

0.431

AC XY:

31963

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.428

AC:

17726

AN:

41390

American (AMR)

AF:

0.361

AC:

5503

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1488

AN:

3466

East Asian (EAS)

AF:

0.339

AC:

1752

AN:

5162

South Asian (SAS)

AF:

0.573

AC:

2759

AN:

4812

European-Finnish (FIN)

AF:

0.492

AC:

5197

AN:

10554

Middle Eastern (MID)

AF:

0.398

AC:

117

AN:

294

European-Non Finnish (NFE)

AF:

0.430

AC:

29190

AN:

67938

Other (OTH)

AF:

0.404

AC:

849

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1855

3710

5566

7421

9276

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

616

1232

1848

2464

3080

<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:

0.430

Hom.:

3386

Bravo

AF:

0.416

Asia WGS

AF:

0.513

AC:

1787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.18

(source)

DANN

Benign

0.47

PhyloP100

-1.5

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