chr2-128151912-C-T

Variant summary

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

The NM_020120.4(UGGT1):​c.2017-872C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,044 control chromosomes in the GnomAD database, including 26,795 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 0.59 ( 26795 hom., cov: 32)

Consequence

UGGT1
NM_020120.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.616

Publications

5 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

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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UGGT1NM_020120.4 linkc.2017-872C>T intron_variant Intron 18 of 40 ENST00000259253.11 NP_064505.1 Q9NYU2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UGGT1ENST00000259253.11 linkc.2017-872C>T intron_variant Intron 18 of 40 1 NM_020120.4 ENSP00000259253.6 Q9NYU2-1
UGGT1ENST00000376723.7 linkn.*2057-872C>T intron_variant Intron 18 of 40 1 ENSP00000365913.3 E2QRN8
UGGT1ENST00000438277.5 linkn.*1605-872C>T intron_variant Intron 16 of 25 1 ENSP00000392701.1 F8WCI2
UGGT1ENST00000488439.1 linkn.317-872C>T intron_variant Intron 1 of 5 5

Frequencies

GnomAD3 genomes
AF:
0.591
AC:
89751
AN:
151924
Hom.:
26775
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.633
Gnomad AMI
AF:
0.521
Gnomad AMR
AF:
0.653
Gnomad ASJ
AF:
0.570
Gnomad EAS
AF:
0.660
Gnomad SAS
AF:
0.428
Gnomad FIN
AF:
0.507
Gnomad MID
AF:
0.589
Gnomad NFE
AF:
0.571
Gnomad OTH
AF:
0.617
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.591
AC:
89825
AN:
152044
Hom.:
26795
Cov.:
32
AF XY:
0.588
AC XY:
43695
AN XY:
74326
show subpopulations
African (AFR)
AF:
0.634
AC:
26268
AN:
41458
American (AMR)
AF:
0.653
AC:
9969
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.570
AC:
1980
AN:
3472
East Asian (EAS)
AF:
0.661
AC:
3421
AN:
5178
South Asian (SAS)
AF:
0.428
AC:
2061
AN:
4820
European-Finnish (FIN)
AF:
0.507
AC:
5359
AN:
10566
Middle Eastern (MID)
AF:
0.605
AC:
178
AN:
294
European-Non Finnish (NFE)
AF:
0.571
AC:
38826
AN:
67962
Other (OTH)
AF:
0.611
AC:
1289
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1879
3758
5638
7517
9396
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
752
1504
2256
3008
3760
<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:
0.506
Hom.:
2076
Bravo
AF:
0.606
Asia WGS
AF:
0.493
AC:
1711
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.66
DANN
Benign
0.20
PhyloP100
-0.62
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs12471108; hg19: chr2-128909486; API