rs3740562

chr10-119177189-G-Achr10-119177189-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006793.5(PRDX3):c.37-36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 1,605,868 control chromosomes in the GnomAD database, including 90,112 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 0.37 (10800 hom., cov: 32)
  • Exomes 𝑓: 0.32 (79312 hom.)
• Consequence: PRDX3 NM_006793.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

Genes affected

PRDX3 (HGNC:9354): (peroxiredoxin 3) This gene encodes a mitochondrial protein with antioxidant function. The protein is similar to the C22 subunit of Salmonella typhimurium alkylhydroperoxide reductase, and it can rescue bacterial resistance to alkylhydroperoxide in E. coli that lack the C22 subunit. The human and mouse genes are highly conserved, and they map to the regions syntenic between mouse and human chromosomes. Sequence comparisons with recently cloned mammalian homologs suggest that these genes consist of a family that is responsible for the regulation of cellular proliferation, differentiation and antioxidant functions. This family member can protect cells from oxidative stress, and it can promote cell survival in prostate cancer. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 1, 3, 13 and 22. [provided by RefSeq, Oct 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDX3	NM_006793.5	c.37-36C>T		intron_variant		ENST00000298510.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDX3	ENST00000298510.4	c.37-36C>T		intron_variant		1	NM_006793.5	P1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55605 AN: 151972 Hom.: 10785 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.349

GnomAD3 exomes AF: 0.324 AC: 78993 AN: 244052 Hom.: 13688 AF XY: 0.319 AC XY: 42421 AN XY: 133088

Gnomad AFR exome AF: 0.483

Gnomad AMR exome AF: 0.213

Gnomad ASJ exome AF: 0.356

Gnomad EAS exome AF: 0.565

Gnomad SAS exome AF: 0.248

Gnomad FIN exome AF: 0.310

Gnomad NFE exome AF: 0.317

Gnomad OTH exome AF: 0.327

GnomAD4 exome AF: 0.325 AC: 472398 AN: 1453778 Hom.: 79312 Cov.: 32 AF XY: 0.322 AC XY: 232992 AN XY: 723408

Gnomad4 AFR exome AF: 0.486

Gnomad4 AMR exome AF: 0.219

Gnomad4 ASJ exome AF: 0.353

Gnomad4 EAS exome AF: 0.541

Gnomad4 SAS exome AF: 0.251

Gnomad4 FIN exome AF: 0.310

Gnomad4 NFE exome AF: 0.322

Gnomad4 OTH exome AF: 0.332

GnomAD4 genome AF: 0.366 AC: 55658 AN: 152090 Hom.: 10800 Cov.: 32 AF XY: 0.363 AC XY: 26974 AN XY: 74352

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.350

Alfa AF: 0.323 Hom.: 8580

Bravo AF: 0.374

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.35
Dann	Benign	0.54

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

LitVar

Other links and lift over

dbSNP: rs3740562; hg19: chr10-120936701;