GeneBe

ENST00000454030.1:n.198-5900C>T

Variant names:

Variant summary

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

The ENST00000454030.1(GULOP):​n.198-5900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,018 control chromosomes in the GnomAD database, including 23,046 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 0.52 ( 23046 hom., cov: 31)

Consequence

GULOP
ENST00000454030.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0580

Publications

12 publications found
Variant links:
Genes affected
GULOP (HGNC:4695): (gulonolactone (L-) oxidase, pseudogene) This gene is nonfunctional in humans and other primates. In most mammalian species the corresponding gene encodes L-gulono-gamma-lactone oxidase which catalyzes the last step of ascorbic acid biosynthesis. The human gene is a remnant that lacks five of twelve exons found in functional rodent genes. The loss of enzyme activity results in hypoascorbemia or the inability to synthesize vitamin C. [provided by RefSeq, Nov 2010]

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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GULOPENST00000454030.1 linkn.198-5900C>T intron_variant Intron 2 of 5 6

Frequencies

GnomAD3 genomes
AF:
0.524
AC:
79550
AN:
151900
Hom.:
23019
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.782
Gnomad AMI
AF:
0.480
Gnomad AMR
AF:
0.416
Gnomad ASJ
AF:
0.507
Gnomad EAS
AF:
0.617
Gnomad SAS
AF:
0.572
Gnomad FIN
AF:
0.360
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.407
Gnomad OTH
AF:
0.524
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.524
AC:
79622
AN:
152018
Hom.:
23046
Cov.:
31
AF XY:
0.522
AC XY:
38750
AN XY:
74290
show subpopulations
African (AFR)
AF:
0.783
AC:
32458
AN:
41478
American (AMR)
AF:
0.416
AC:
6361
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.507
AC:
1761
AN:
3472
East Asian (EAS)
AF:
0.617
AC:
3172
AN:
5142
South Asian (SAS)
AF:
0.571
AC:
2750
AN:
4812
European-Finnish (FIN)
AF:
0.360
AC:
3801
AN:
10568
Middle Eastern (MID)
AF:
0.497
AC:
146
AN:
294
European-Non Finnish (NFE)
AF:
0.407
AC:
27639
AN:
67934
Other (OTH)
AF:
0.518
AC:
1096
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1735
3470
5205
6940
8675
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
686
1372
2058
2744
3430
<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:
0.448
Hom.:
54150
Bravo
AF:
0.539
Asia WGS
AF:
0.573
AC:
1996
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.1
DANN
Benign
0.53
PhyloP100
-0.058

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1316801; hg19: chr8-27429228; API