Genetic Variant PRDX6:c.*15C>T (chr1-173487878-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_004905.3(PRDX6):c.*15C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,611,100 control chromosomes in the GnomAD database, including 65,943 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 ( 12300 hom., cov: 32)

Exomes 𝑓: 0.26 ( 53643 hom. )

Consequence

PRDX6
NM_004905.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.56

Publications

11 publications found

Variant links:

Genes affected

PRDX6 (HGNC:16753): (peroxiredoxin 6) The protein encoded by this gene is a member of the thiol-specific antioxidant protein family. This protein is a bifunctional enzyme with two distinct active sites. It is involved in redox regulation of the cell; it can reduce H(2)O(2) and short chain organic, fatty acid, and phospholipid hydroperoxides. It may play a role in the regulation of phospholipid turnover as well as in protection against oxidative injury. [provided by RefSeq, Jul 2008]

PRDX6 links:

PRDX6-AS1 (HGNC:54870): (PRDX6 antisense RNA 1)

PRDX6-AS1 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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX6	NM_004905.3 link	c.*15C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000340385.6	NP_004896.1	P30041V9HWC7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX6	ENST00000340385.6 link	c.*15C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_004905.3	ENSP00000342026.5		P30041

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54573

AN:

152014

Hom.:

12247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.626

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.597

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.317

GnomAD2 exomes

AF:

0.284

AC:

71180

AN:

250328

AF XY:

0.276

show subpopulations

Gnomad AFR exome

AF:

0.635

Gnomad AMR exome

AF:

0.188

Gnomad ASJ exome

AF:

0.329

Gnomad EAS exome

AF:

0.615

Gnomad FIN exome

AF:

0.200

Gnomad NFE exome

AF:

0.242

Gnomad OTH exome

AF:

0.271

GnomAD4 exome

AF:

0.257

AC:

375251

AN:

1458968

Hom.:

53643

Cov.:

AF XY:

0.255

AC XY:

185246

AN XY:

725728

show subpopulations

African (AFR)

AF:

0.638

AC:

21281

AN:

33376

American (AMR)

AF:

0.193

AC:

8597

AN:

44624

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

8593

AN:

26110

East Asian (EAS)

AF:

0.575

AC:

22826

AN:

39678

South Asian (SAS)

AF:

0.213

AC:

18296

AN:

86078

European-Finnish (FIN)

AF:

0.200

AC:

10698

AN:

53368

Middle Eastern (MID)

AF:

0.315

AC:

1336

AN:

4238

European-Non Finnish (NFE)

AF:

0.240

AC:

266395

AN:

1111316

Other (OTH)

AF:

0.286

AC:

17229

AN:

60180

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

12926

25851

38777

51702

64628

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9384

18768

28152

37536

46920

<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:

54696

AN:

152132

Hom.:

12300

Cov.:

AF XY:

0.355

AC XY:

26430

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.627

AC:

25995

AN:

41482

American (AMR)

AF:

0.256

AC:

3914

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.340

AC:

1180

AN:

3470

East Asian (EAS)

AF:

0.597

AC:

3090

AN:

5172

South Asian (SAS)

AF:

0.217

AC:

1045

AN:

4826

European-Finnish (FIN)

AF:

0.198

AC:

2097

AN:

10578

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16351

AN:

68000

Other (OTH)

AF:

0.320

AC:

674

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1567

3134

4701

6268

7835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

488

976

1464

1952

2440

<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:

0.403

Hom.:

4252

Bravo

AF:

0.378

Asia WGS

AF:

0.432

AC:

1500

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.80

(source)

DANN

Benign

0.55

PhyloP100

-3.6

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