dbSNP rs2000: PRDX6:c.*832G>A (chr1-173488695-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_004905.3(PRDX6):c.*832G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 152,326 control chromosomes in the GnomAD database, including 51 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 0.020 ( 51 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

PRDX6
NM_004905.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.61

Publications

39 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:

LOC124904456 (HGNC:):

LOC124904456 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=-0.81).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0204 (3113/152326) while in subpopulation NFE AF = 0.0317 (2155/68026). AF 95% confidence interval is 0.0306. There are 51 homozygotes in GnomAd4. There are 1456 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 51 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX6	NM_004905.3 link	c.*832G>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000340385.6	NP_004896.1
LOC124904456	XR_007066738.1 link	n.*68C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
PRDX6	ENST00000340385.6 link	c.*832G>A	3_prime_UTR_variant	Exon 5 of 5	1	NM_004905.3	ENSP00000342026.5
PRDX6-AS1	ENST00000669220.1 link	n.117+596C>T	intron_variant	Intron 1 of 3
PRDX6-AS1	ENST00000778745.1 link	n.112+596C>T	intron_variant	Intron 1 of 2
PRDX6-AS1	ENST00000778747.1 link	n.114+596C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0205

AC:

3117

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00564

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.0228

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.00972

Gnomad FIN

AF:

0.0111

Gnomad MID

AF:

0.0605

Gnomad NFE

AF:

0.0317

Gnomad OTH

AF:

0.0267

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0204

AC:

3113

AN:

152326

Hom.:

Cov.:

AF XY:

0.0195

AC XY:

1456

AN XY:

74496

show subpopulations

African (AFR)

AF:

0.00560

AC:

233

AN:

41576

American (AMR)

AF:

0.0227

AC:

348

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3466

East Asian (EAS)

AF:

0.000578

AC:

AN:

5188

South Asian (SAS)

AF:

0.00973

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0111

AC:

118

AN:

10618

Middle Eastern (MID)

AF:

0.0582

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0317

AC:

2155

AN:

68026

Other (OTH)

AF:

0.0260

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

170

339

509

678

848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<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:

0.0282

Hom.:

Bravo

AF:

0.0209

Asia WGS

AF:

0.00577

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.9

(source)

DANN

Benign

0.43

PhyloP100

1.6

Mutation Taster

=100/0

polymorphism

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over