dbSNP rs7768: PRDX3:n.2065C>G (chr10-119168281-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000494433.1(PRDX3):n.2065C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,102,234 control chromosomes in the GnomAD database, including 64,826 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 0.36 ( 10357 hom., cov: 33)

Exomes 𝑓: 0.33 ( 54469 hom. )

Consequence

PRDX3
ENST00000494433.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.493

Publications

17 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

PRDX3 links:

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX3	NM_006793.5 link	c.*199C>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000298510.4	NP_006784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX3	ENST00000494433.1 link	n.2065C>G		non_coding_transcript_exon_variant	Exon 2 of 2	1
PRDX3	ENST00000298510.4 link	c.*199C>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_006793.5	ENSP00000298510.2

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54735

AN:

151896

Hom.:

10345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.451

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.278

Gnomad ASJ

AF:

0.389

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.341

GnomAD4 exome

AF:

0.333

AC:

316153

AN:

950220

Hom.:

54469

Cov.:

AF XY:

0.330

AC XY:

155623

AN XY:

472132

show subpopulations

African (AFR)

AF:

0.457

AC:

9284

AN:

20306

American (AMR)

AF:

0.239

AC:

3464

AN:

14508

Ashkenazi Jewish (ASJ)

AF:

0.365

AC:

6063

AN:

16616

East Asian (EAS)

AF:

0.549

AC:

15715

AN:

28648

South Asian (SAS)

AF:

0.253

AC:

13080

AN:

51606

European-Finnish (FIN)

AF:

0.309

AC:

8645

AN:

28000

Middle Eastern (MID)

AF:

0.302

AC:

880

AN:

2914

European-Non Finnish (NFE)

AF:

0.328

AC:

245048

AN:

746240

Other (OTH)

AF:

0.338

AC:

13974

AN:

41382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

9801

19602

29402

39203

49004

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7684

15368

23052

30736

38420

<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:

0.360

AC:

54783

AN:

152014

Hom.:

10357

Cov.:

AF XY:

0.357

AC XY:

26537

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.450

AC:

18673

AN:

41468

American (AMR)

AF:

0.278

AC:

4247

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.389

AC:

1351

AN:

3470

East Asian (EAS)

AF:

0.553

AC:

2869

AN:

5184

South Asian (SAS)

AF:

0.271

AC:

1305

AN:

4812

European-Finnish (FIN)

AF:

0.315

AC:

3321

AN:

10552

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.322

AC:

21864

AN:

67946

Other (OTH)

AF:

0.343

AC:

725

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1839

3678

5518

7357

9196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

520

1040

1560

2080

2600

<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:

0.178

Hom.:

332

Bravo

AF:

0.367

Asia WGS

AF:

0.379

AC:

1318

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.4

(source)

DANN

Benign

0.49

PhyloP100

0.49

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over