Genetic Variant PRDX2:n.761A>G (chr19-12800471-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000466174.5(PRDX2):n.761A>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 0.13 in 909,506 control chromosomes in the GnomAD database, including 12,083 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 0.21 ( 5584 hom., cov: 31)

Exomes 𝑓: 0.11 ( 6499 hom. )

Consequence

PRDX2
ENST00000466174.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.16

Publications

7 publications found

Variant links:

Genes affected

PRDX2 (HGNC:9353): (peroxiredoxin 2) This gene encodes a member of the peroxiredoxin family of antioxidant enzymes, which reduce hydrogen peroxide and alkyl hydroperoxides. The encoded protein plays an antioxidant protective role in cells, and it may contribute to the antiviral activity of CD8(+) T-cells. The crystal structure of this protein has been resolved to 2.7 angstroms. This protein prevents hemolytic anemia from oxidative stress by stabilizing hemoglobin, thus making this gene a therapeutic target for patients with hemolytic anemia. This protein may have a proliferative effect and play a role in cancer development or progression. Related pseudogenes have been identified on chromosomes 5, 6, 10 and 13. [provided by RefSeq, Mar 2013]

PRDX2 links:

ENSG00000267062 (HGNC:):

ENSG00000267062 links:

HOOK2 (HGNC:19885): (hook microtubule tethering protein 2) Hook proteins are cytosolic coiled-coil proteins that contain conserved N-terminal domains, which attach to microtubules, and more divergent C-terminal domains, which mediate binding to organelles. The Drosophila Hook protein is a component of the endocytic compartment.[supplied by OMIM, Apr 2004]

HOOK2 links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX2	NM_005809.6 link	c.258-172A>G		intron_variant	Intron 3 of 5	ENST00000301522.3	NP_005800.3	P32119-1V9HW12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX2	ENST00000301522.3 link	c.258-172A>G		intron_variant	Intron 3 of 5	1	NM_005809.6	ENSP00000301522.2		P32119-1

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32108

AN:

151930

Hom.:

5561

Cov.:

show subpopulations

Gnomad AFR

AF:

0.475

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.0913

Gnomad EAS

AF:

0.0605

Gnomad SAS

AF:

0.0934

Gnomad FIN

AF:

0.0821

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.176

GnomAD4 exome

AF:

0.113

AC:

85968

AN:

757458

Hom.:

6499

Cov.:

AF XY:

0.112

AC XY:

42952

AN XY:

382220

show subpopulations

African (AFR)

AF:

0.485

AC:

8733

AN:

18008

American (AMR)

AF:

0.174

AC:

3223

AN:

18482

Ashkenazi Jewish (ASJ)

AF:

0.0933

AC:

1443

AN:

15474

East Asian (EAS)

AF:

0.0753

AC:

2442

AN:

32450

South Asian (SAS)

AF:

0.102

AC:

5301

AN:

51928

European-Finnish (FIN)

AF:

0.0788

AC:

2983

AN:

37872

Middle Eastern (MID)

AF:

0.117

AC:

377

AN:

3216

European-Non Finnish (NFE)

AF:

0.105

AC:

56938

AN:

544218

Other (OTH)

AF:

0.126

AC:

4528

AN:

35810

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3530

7060

10589

14119

17649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1652

3304

4956

6608

8260

<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:

0.212

AC:

32174

AN:

152048

Hom.:

5584

Cov.:

AF XY:

0.206

AC XY:

15352

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.476

AC:

19708

AN:

41432

American (AMR)

AF:

0.176

AC:

2690

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0913

AC:

317

AN:

3472

East Asian (EAS)

AF:

0.0604

AC:

312

AN:

5162

South Asian (SAS)

AF:

0.0939

AC:

453

AN:

4824

European-Finnish (FIN)

AF:

0.0821

AC:

871

AN:

10608

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7293

AN:

67972

Other (OTH)

AF:

0.174

AC:

366

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1074

2147

3221

4294

5368

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.196

Hom.:

1928

Bravo

AF:

0.230

Asia WGS

AF:

0.107

AC:

373

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.0

(source)

DANN

Benign

0.55

PhyloP100

-3.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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