chr10-119168032-T-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006793.5(PRDX3):c.*448A>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 0.438 in 159,848 control chromosomes in the GnomAD database, including 17,681 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 0.44 ( 16612 hom., cov: 33)
Exomes 𝑓: 0.50 ( 1069 hom. )
Consequence
PRDX3
NM_006793.5 3_prime_UTR
NM_006793.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.780
Publications
20 publications found
Genes affected
PRDX3 (HGNC:9354): (peroxiredoxin 3) This gene encodes a mitochondrial protein with antioxidant function. The protein is similar to the C22 subunit of Salmonella typhimurium alkylhydroperoxide reductase, and it can rescue bacterial resistance to alkylhydroperoxide in E. coli that lack the C22 subunit. The human and mouse genes are highly conserved, and they map to the regions syntenic between mouse and human chromosomes. Sequence comparisons with recently cloned mammalian homologs suggest that these genes consist of a family that is responsible for the regulation of cellular proliferation, differentiation and antioxidant functions. This family member can protect cells from oxidative stress, and it can promote cell survival in prostate cancer. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 1, 3, 13 and 22. [provided by RefSeq, Oct 2014]
PRDX3 Gene-Disease associations (from GenCC):
- corneal dystrophy, punctiform and polychromatic pre-descemetInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- spinocerebellar ataxia, autosomal recessive 32Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRDX3 | NM_006793.5 | c.*448A>C | 3_prime_UTR_variant | Exon 7 of 7 | ENST00000298510.4 | NP_006784.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.436 AC: 66230AN: 152020Hom.: 16606 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
66230
AN:
152020
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.500 AC: 3853AN: 7710Hom.: 1069 Cov.: 0 AF XY: 0.497 AC XY: 1919AN XY: 3860 show subpopulations
GnomAD4 exome
AF:
AC:
3853
AN:
7710
Hom.:
Cov.:
0
AF XY:
AC XY:
1919
AN XY:
3860
show subpopulations
African (AFR)
AF:
AC:
8
AN:
60
American (AMR)
AF:
AC:
69
AN:
158
Ashkenazi Jewish (ASJ)
AF:
AC:
53
AN:
128
East Asian (EAS)
AF:
AC:
25
AN:
96
South Asian (SAS)
AF:
AC:
431
AN:
890
European-Finnish (FIN)
AF:
AC:
292
AN:
502
Middle Eastern (MID)
AF:
AC:
22
AN:
34
European-Non Finnish (NFE)
AF:
AC:
2686
AN:
5306
Other (OTH)
AF:
AC:
267
AN:
536
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
85
171
256
342
427
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
10
20
30
40
50
<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: 0.435 AC: 66232AN: 152138Hom.: 16612 Cov.: 33 AF XY: 0.439 AC XY: 32674AN XY: 74370 show subpopulations
GnomAD4 genome
AF:
AC:
66232
AN:
152138
Hom.:
Cov.:
33
AF XY:
AC XY:
32674
AN XY:
74370
show subpopulations
African (AFR)
AF:
AC:
7553
AN:
41534
American (AMR)
AF:
AC:
7638
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
1645
AN:
3472
East Asian (EAS)
AF:
AC:
1723
AN:
5176
South Asian (SAS)
AF:
AC:
2635
AN:
4826
European-Finnish (FIN)
AF:
AC:
6238
AN:
10552
Middle Eastern (MID)
AF:
AC:
113
AN:
294
European-Non Finnish (NFE)
AF:
AC:
37194
AN:
67992
Other (OTH)
AF:
AC:
978
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1738
3476
5213
6951
8689
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
612
1224
1836
2448
3060
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1603
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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