dbSNP rs552105: PRDX4:c.600-40G>A (chrX-23682356-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_006406.2(PRDX4):c.600-40G>A 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 0.60 ( 14284 hom., 18083 hem., cov: 20)

Exomes 𝑓: 0.58 ( 112004 hom. 160330 hem. )

Failed GnomAD Quality Control

Consequence

PRDX4
NM_006406.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.363

Publications

11 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: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX4	NM_006406.2 link	c.600-40G>A		intron_variant	Intron 4 of 6	ENST00000379341.9	NP_006397.1	Q13162V9HW63

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX4	ENST00000379341.9 link	c.600-40G>A		intron_variant	Intron 4 of 6	1	NM_006406.2	ENSP00000368646.4		Q13162
PRDX4	ENST00000439422.1 link	c.231-40G>A		intron_variant	Intron 2 of 5	3		ENSP00000413736.1		H7C3T4

Frequencies

GnomAD3 genomes

AF:

0.600

AC:

64846

AN:

108024

Hom.:

14285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.729

Gnomad AMR

AF:

0.673

Gnomad ASJ

AF:

0.731

Gnomad EAS

AF:

0.737

Gnomad SAS

AF:

0.583

Gnomad FIN

AF:

0.508

Gnomad MID

AF:

0.674

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.602

GnomAD2 exomes

AF:

0.602

AC:

84322

AN:

140013

AF XY:

0.581

show subpopulations

Gnomad AFR exome

AF:

0.618

Gnomad AMR exome

AF:

0.694

Gnomad ASJ exome

AF:

0.712

Gnomad EAS exome

AF:

0.746

Gnomad FIN exome

AF:

0.523

Gnomad NFE exome

AF:

0.564

Gnomad OTH exome

AF:

0.594

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.577

AC:

544813

AN:

944921

Hom.:

112004

Cov.:

AF XY:

0.576

AC XY:

160330

AN XY:

278193

show subpopulations

African (AFR)

AF:

0.608

AC:

13130

AN:

21611

American (AMR)

AF:

0.695

AC:

17462

AN:

25113

Ashkenazi Jewish (ASJ)

AF:

0.730

AC:

10384

AN:

14225

East Asian (EAS)

AF:

0.736

AC:

16619

AN:

22583

South Asian (SAS)

AF:

0.584

AC:

25269

AN:

43281

European-Finnish (FIN)

AF:

0.524

AC:

16799

AN:

32057

Middle Eastern (MID)

AF:

0.654

AC:

2202

AN:

3366

European-Non Finnish (NFE)

AF:

0.565

AC:

420642

AN:

745044

Other (OTH)

AF:

0.593

AC:

22306

AN:

37641

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

6937

13875

20812

27750

34687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14220

28440

42660

56880

71100

<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

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.600

AC:

64871

AN:

108081

Hom.:

14284

Cov.:

AF XY:

0.594

AC XY:

18083

AN XY:

30443

show subpopulations

African (AFR)

AF:

0.618

AC:

18301

AN:

29631

American (AMR)

AF:

0.672

AC:

6694

AN:

9956

Ashkenazi Jewish (ASJ)

AF:

0.731

AC:

1910

AN:

2614

East Asian (EAS)

AF:

0.737

AC:

2483

AN:

3369

South Asian (SAS)

AF:

0.582

AC:

1450

AN:

2490

European-Finnish (FIN)

AF:

0.508

AC:

2792

AN:

5493

Middle Eastern (MID)

AF:

0.689

AC:

144

AN:

209

European-Non Finnish (NFE)

AF:

0.570

AC:

29728

AN:

52194

Other (OTH)

AF:

0.606

AC:

892

AN:

1471

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

922

1845

2767

3690

4612

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

568

1136

1704

2272

2840

<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:

0.597

Hom.:

7373

Bravo

AF:

0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

0.36

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