GeneBe

8-104330599-G-C

Variant names:

Variant summary

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

The ENST00000521601.1(DPYS):​n.476-162C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,998 control chromosomes in the GnomAD database, including 28,543 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 ( 28543 hom., cov: 33)

Consequence

DPYS
ENST00000521601.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.436

Publications

5 publications found
Variant links:
Genes affected
DPYS (HGNC:3013): (dihydropyrimidinase) Dihydropyrimidinase catalyzes the conversion of 5,6-dihydrouracil to 3-ureidopropionate in pyrimidine metabolism. Dihydropyrimidinase is expressed at a high level in liver and kidney as a major 2.5-kb transcript and a minor 3.8-kb transcript. Defects in the DPYS gene are linked to dihydropyrimidinuria. [provided by RefSeq, Jul 2008]
DPYS Gene-Disease associations (from GenCC):
  • dihydropyrimidinuria
    Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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
DPYSENST00000521601.1 linkn.476-162C>G intron_variant Intron 4 of 4 4

Frequencies

GnomAD3 genomes
AF:
0.589
AC:
89466
AN:
151884
Hom.:
28482
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.814
Gnomad AMI
AF:
0.427
Gnomad AMR
AF:
0.651
Gnomad ASJ
AF:
0.440
Gnomad EAS
AF:
0.860
Gnomad SAS
AF:
0.557
Gnomad FIN
AF:
0.477
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.448
Gnomad OTH
AF:
0.573
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.589
AC:
89591
AN:
151998
Hom.:
28543
Cov.:
33
AF XY:
0.590
AC XY:
43874
AN XY:
74300
show subpopulations
African (AFR)
AF:
0.814
AC:
33802
AN:
41508
American (AMR)
AF:
0.651
AC:
9937
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.440
AC:
1525
AN:
3468
East Asian (EAS)
AF:
0.860
AC:
4449
AN:
5174
South Asian (SAS)
AF:
0.558
AC:
2680
AN:
4806
European-Finnish (FIN)
AF:
0.477
AC:
5016
AN:
10506
Middle Eastern (MID)
AF:
0.507
AC:
148
AN:
292
European-Non Finnish (NFE)
AF:
0.448
AC:
30432
AN:
67972
Other (OTH)
AF:
0.578
AC:
1213
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1701
3401
5102
6802
8503
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
720
1440
2160
2880
3600
<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.:
2444
Bravo
AF:
0.611
Asia WGS
AF:
0.750
AC:
2607
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.69
DANN
Benign
0.33
PhyloP100
-0.44

Splicing

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

Publications

Other links and lift over

dbSNP: rs7010076; hg19: chr8-105342827; API