10-119168281-G-C

Position:

• chr10-119168281-G-C

Variant summary

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

The NM_006793.5(PRDX3):​c.*199C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,102,234 control chromosomes in the GnomAD database, including 64,826 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 (10357 hom., cov: 33)
  • Exomes 𝑓: 0.33 (54469 hom.)
• Consequence: PRDX3 NM_006793.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRDX3	NM_006793.5	c.*199C>G		3_prime_UTR_variant	7/7	ENST00000298510.4	NP_006784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDX3	ENST00000298510.4	c.*199C>G		3_prime_UTR_variant	7/7	1	NM_006793.5	ENSP00000298510	P1
PRDX3	ENST00000494433.1	n.2065C>G		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54735 AN: 151896 Hom.: 10345 Cov.: 33

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.333 AC: 316153 AN: 950220 Hom.: 54469 Cov.: 12 AF XY: 0.330 AC XY: 155623 AN XY: 472132

Gnomad4 AFR exome AF: 0.457

Gnomad4 AMR exome AF: 0.239

Gnomad4 ASJ exome AF: 0.365

Gnomad4 EAS exome AF: 0.549

Gnomad4 SAS exome AF: 0.253

Gnomad4 FIN exome AF: 0.309

Gnomad4 NFE exome AF: 0.328

Gnomad4 OTH exome AF: 0.338

GnomAD4 genome AF: 0.360 AC: 54783 AN: 152014 Hom.: 10357 Cov.: 33 AF XY: 0.357 AC XY: 26537 AN XY: 74298

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.343

Alfa AF: 0.178 Hom.: 332

Bravo AF: 0.367

Asia WGS AF: 0.379 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7768; hg19: chr10-120927793; COSMIC: COSV53719661; COSMIC: COSV53719661;