rs4611

Variant names:

• chr1-173487878-C-T
• rs4611
• NM_004905.3:c.*15C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56
• Publications: 11 publications found

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004905.3. 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.*15C>T		3_prime_UTR	Exon 5 of 5	NP_004896.1	P30041

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX6	ENST00000340385.6	TSL:1 MANE Select	c.*15C>T		3_prime_UTR	Exon 5 of 5	ENSP00000342026.5	P30041
	PRDX6	ENST00000922555.1		c.*15C>T		3_prime_UTR	Exon 6 of 6	ENSP00000592614.1
	PRDX6	ENST00000867927.1		c.*15C>T		3_prime_UTR	Exon 6 of 6	ENSP00000537986.1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54573 AN: 152014 Hom.: 12247 Cov.: 32

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

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.: 33 AF XY: 0.255 AC XY: 185246 AN XY: 725728

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

GnomAD4 genome AF: 0.360 AC: 54696 AN: 152132 Hom.: 12300 Cov.: 32 AF XY: 0.355 AC XY: 26430 AN XY: 74388

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: 91 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16351 AN: 68000

Other (OTH) AF: 0.320 AC: 674 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.80
DANN	Benign	0.55
PhyloP100		-3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4611; hg19: chr1-173457017; COSMIC: COSV61165110;