Genetic Variant PRDX4:c.730+50A>G (chrX-23682576-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006406.2(PRDX4):c.730+50A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.39 ( 6229 hom., 11416 hem., cov: 20)

Exomes 𝑓: 0.42 ( 56408 hom. 104516 hem. )

Consequence

PRDX4
NM_006406.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.26

Publications

10 publications found

Variant links:

Genes affected

PRDX4 (HGNC:17169): (peroxiredoxin 4) The protein encoded by this gene is an antioxidant enzyme and belongs to the peroxiredoxin family. The protein is localized to the cytoplasm. Peroxidases of the peroxiredoxin family reduce hydrogen peroxide and alkyl hydroperoxides to water and alcohol with the use of reducing equivalents derived from thiol-containing donor molecules. This protein has been found to play a regulatory role in the activation of the transcription factor NF-kappaB. [provided by RefSeq, Jul 2008]

PRDX4 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006406.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX4	NM_006406.2	MANE Select	c.730+50A>G		intron	N/A	NP_006397.1	Q13162

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PRDX4	ENST00000379341.9	TSL:1 MANE Select	c.730+50A>G	intron	N/A	ENSP00000368646.4	Q13162
PRDX4	ENST00000931168.1		c.844+50A>G	intron	N/A	ENSP00000601227.1
PRDX4	ENST00000887283.1		c.688+50A>G	intron	N/A	ENSP00000557342.1

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

42067

AN:

107058

Hom.:

6233

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.463

Gnomad ASJ

AF:

0.515

Gnomad EAS

AF:

0.494

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.419

Gnomad MID

AF:

0.498

Gnomad NFE

AF:

0.412

Gnomad OTH

AF:

0.422

GnomAD2 exomes

AF:

0.430

AC:

53578

AN:

124571

AF XY:

0.423

show subpopulations

Gnomad AFR exome

AF:

0.312

Gnomad AMR exome

AF:

0.543

Gnomad ASJ exome

AF:

0.498

Gnomad EAS exome

AF:

0.509

Gnomad FIN exome

AF:

0.428

Gnomad NFE exome

AF:

0.418

Gnomad OTH exome

AF:

0.434

GnomAD4 exome

AF:

0.421

AC:

372512

AN:

885835

Hom.:

56408

Cov.:

AF XY:

0.441

AC XY:

104516

AN XY:

237089

show subpopulations

African (AFR)

AF:

0.311

AC:

6203

AN:

19967

American (AMR)

AF:

0.545

AC:

11329

AN:

20795

Ashkenazi Jewish (ASJ)

AF:

0.515

AC:

7055

AN:

13688

East Asian (EAS)

AF:

0.505

AC:

11209

AN:

22188

South Asian (SAS)

AF:

0.361

AC:

13501

AN:

37422

European-Finnish (FIN)

AF:

0.432

AC:

14096

AN:

32650

Middle Eastern (MID)

AF:

0.481

AC:

1615

AN:

3361

European-Non Finnish (NFE)

AF:

0.418

AC:

292177

AN:

699740

Other (OTH)

AF:

0.425

AC:

15327

AN:

36024

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

6853

13707

20560

27414

34267

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10322

20644

30966

41288

51610

<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:

0.393

AC:

42076

AN:

107103

Hom.:

6229

Cov.:

AF XY:

0.386

AC XY:

11416

AN XY:

29611

show subpopulations

African (AFR)

AF:

0.311

AC:

9165

AN:

29485

American (AMR)

AF:

0.463

AC:

4491

AN:

9692

Ashkenazi Jewish (ASJ)

AF:

0.515

AC:

1339

AN:

2598

East Asian (EAS)

AF:

0.493

AC:

1666

AN:

3382

South Asian (SAS)

AF:

0.346

AC:

844

AN:

2440

European-Finnish (FIN)

AF:

0.419

AC:

2154

AN:

5140

Middle Eastern (MID)

AF:

0.519

AC:

110

AN:

212

European-Non Finnish (NFE)

AF:

0.412

AC:

21429

AN:

52061

Other (OTH)

AF:

0.426

AC:

615

AN:

1443

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

914

1829

2743

3658

4572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.386

Hom.:

11199

Bravo

AF:

0.400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.3

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over