Genetic Variant PRDX6:c.*1095G>C (chr1-173488958-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000867927.1(PRDX6):c.*1095G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0261 in 152,252 control chromosomes in the GnomAD database, including 66 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 0.026 ( 66 hom., cov: 32)

Consequence

PRDX6
ENST00000867927.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.47

Publications

1 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:

LOC124904456 (HGNC:):

LOC124904456 links:

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

PRDX6-AS1 links:

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new If you want to explore the variant's impact on the transcript ENST00000867927.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.9).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0261 (3969/152252) while in subpopulation NFE AF = 0.042 (2857/68012). AF 95% confidence interval is 0.0407. There are 66 homozygotes in GnomAd4. There are 1886 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 66 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000867927.1. 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
	PRDX6	NM_004905.3	MANE Select	c.*1095G>C		downstream_gene	N/A	NP_004896.1	P30041

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
PRDX6	ENST00000867927.1	c.*1095G>C	3_prime_UTR	Exon 6 of 6	ENSP00000537986.1
PRDX6-AS1	ENST00000669220.1	n.117+333C>G	intron	N/A
PRDX6-AS1	ENST00000778745.1	n.112+333C>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0261

AC:

3970

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00763

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.0143

Gnomad ASJ

AF:

0.0406

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00994

Gnomad FIN

AF:

0.0263

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0420

Gnomad OTH

AF:

0.0206

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0261

AC:

3969

AN:

152252

Hom.:

Cov.:

AF XY:

0.0253

AC XY:

1886

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.00761

AC:

316

AN:

41540

American (AMR)

AF:

0.0143

AC:

218

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0406

AC:

141

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5192

South Asian (SAS)

AF:

0.00995

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.0263

AC:

279

AN:

10604

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0420

AC:

2857

AN:

68012

Other (OTH)

AF:

0.0204

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

212

424

635

847

1059

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.0160

Hom.:

Bravo

AF:

0.0247

Asia WGS

AF:

0.00433

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.020

(source)

DANN

Benign

0.47

PhyloP100

-2.5

Splicing

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over