NM_006793.5:c.*448A>C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.780

Publications

20 publications found
Variant links:
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-descemet
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • spinocerebellar ataxia, autosomal recessive 32
    Inheritance: 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
PRDX3NM_006793.5 linkc.*448A>C 3_prime_UTR_variant Exon 7 of 7 ENST00000298510.4 NP_006784.1 P30048-1A0A384MTR2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRDX3ENST00000298510.4 linkc.*448A>C 3_prime_UTR_variant Exon 7 of 7 1 NM_006793.5 ENSP00000298510.2 P30048-1
PRDX3ENST00000494433.1 linkn.*37A>C downstream_gene_variant 1

Frequencies

GnomAD3 genomes
AF:
0.436
AC:
66230
AN:
152020
Hom.:
16606
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.182
Gnomad AMI
AF:
0.567
Gnomad AMR
AF:
0.499
Gnomad ASJ
AF:
0.474
Gnomad EAS
AF:
0.334
Gnomad SAS
AF:
0.545
Gnomad FIN
AF:
0.591
Gnomad MID
AF:
0.402
Gnomad NFE
AF:
0.547
Gnomad OTH
AF:
0.465
GnomAD4 exome
AF:
0.500
AC:
3853
AN:
7710
Hom.:
1069
Cov.:
0
AF XY:
0.497
AC XY:
1919
AN XY:
3860
show subpopulations
African (AFR)
AF:
0.133
AC:
8
AN:
60
American (AMR)
AF:
0.437
AC:
69
AN:
158
Ashkenazi Jewish (ASJ)
AF:
0.414
AC:
53
AN:
128
East Asian (EAS)
AF:
0.260
AC:
25
AN:
96
South Asian (SAS)
AF:
0.484
AC:
431
AN:
890
European-Finnish (FIN)
AF:
0.582
AC:
292
AN:
502
Middle Eastern (MID)
AF:
0.647
AC:
22
AN:
34
European-Non Finnish (NFE)
AF:
0.506
AC:
2686
AN:
5306
Other (OTH)
AF:
0.498
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:
66232
AN:
152138
Hom.:
16612
Cov.:
33
AF XY:
0.439
AC XY:
32674
AN XY:
74370
show subpopulations
African (AFR)
AF:
0.182
AC:
7553
AN:
41534
American (AMR)
AF:
0.500
AC:
7638
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.474
AC:
1645
AN:
3472
East Asian (EAS)
AF:
0.333
AC:
1723
AN:
5176
South Asian (SAS)
AF:
0.546
AC:
2635
AN:
4826
European-Finnish (FIN)
AF:
0.591
AC:
6238
AN:
10552
Middle Eastern (MID)
AF:
0.384
AC:
113
AN:
294
European-Non Finnish (NFE)
AF:
0.547
AC:
37194
AN:
67992
Other (OTH)
AF:
0.464
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:
0.500
Hom.:
72862
Bravo
AF:
0.412
Asia WGS
AF:
0.462
AC:
1603
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.60
DANN
Benign
0.34
PhyloP100
-0.78
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: rs3377; hg19: chr10-120927544; API