rs17522918

Positions:

• chr1-45521902-C-A
• chr1-45521902-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001202431.2(PRDX1):​c.-12+876G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,590 control chromosomes in the GnomAD database, including 952 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 0.10 (949 hom., cov: 32)
  • Exomes 𝑓: 0.077 (3 hom.)
• Consequence: PRDX1 NM_001202431.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

Genes affected

PRDX1 (HGNC:9352): (peroxiredoxin 1) This gene encodes a member of the peroxiredoxin family of antioxidant enzymes, which reduce hydrogen peroxide and alkyl hydroperoxides. The encoded protein may play an antioxidant protective role in cells, and may contribute to the antiviral activity of CD8(+) T-cells. This protein may have a proliferative effect and play a role in cancer development or progression. Four transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRDX1	NM_001202431.2	c.-12+876G>T		intron_variant			NP_001189360.1
PRDX1	NM_181697.3	c.-85G>T		upstream_gene_variant		ENST00000319248.13	NP_859048.1
PRDX1	NM_002574.4	c.-305G>T		upstream_gene_variant			NP_002565.1
PRDX1	NM_181696.3	c.-279G>T		upstream_gene_variant			NP_859047.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDX1	ENST00000319248.13	c.-85G>T		upstream_gene_variant		1	NM_181697.3	ENSP00000361152.5

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15876 AN: 152056 Hom.: 942 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0736

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.117

GnomAD4 exome AF: 0.0769 AC: 32 AN: 416 Hom.: 3 Cov.: 0 AF XY: 0.0648 AC XY: 21 AN XY: 324

Gnomad4 AFR exome AF: 0.100

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.0656

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.104 AC: 15897 AN: 152174 Hom.: 949 Cov.: 32 AF XY: 0.105 AC XY: 7823 AN XY: 74378

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0737

Gnomad4 FIN AF: 0.0893

Gnomad4 NFE AF: 0.0942

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0940 Hom.: 815

Bravo AF: 0.112

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	7.5
DANN	Benign	0.73

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: rs17522918; hg19: chr1-45987574;