ENST00000262746.5:c.-305G>T

Variant names:

• chr1-45521902-C-A
• rs17522918
• ENST00000262746.5:c.-305G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000262746.5(PRDX1):​c.-305G>T variant causes a 5 prime UTR 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 ENST00000262746.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841
• Publications: 20 publications found

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]

PRDX1 Gene-Disease associations (from GenCC):

• methylmalonic aciduria and homocystinuria type cblC

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000298796 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000262746.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX1	NM_001202431.2		c.-12+876G>T		intron	N/A	NP_001189360.1
	PRDX1	NM_181697.3	MANE Select	c.-85G>T		upstream_gene	N/A	NP_859048.1
	PRDX1	NM_002574.4		c.-305G>T		upstream_gene	N/A	NP_002565.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX1	ENST00000262746.5	TSL:5	c.-305G>T		5_prime_UTR	Exon 1 of 6	ENSP00000262746.1
	PRDX1	ENST00000447184.6	TSL:5	c.-56G>T		5_prime_UTR	Exon 1 of 6	ENSP00000407034.2
	PRDX1	ENST00000424390.2	TSL:2	c.-12+876G>T		intron	N/A	ENSP00000389047.2

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

African (AFR) AF: 0.100 AC: 1 AN: 10

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.152 AC: 7 AN: 46

Middle Eastern (MID) AF: 0.167 AC: 1 AN: 6

European-Non Finnish (NFE) AF: 0.0656 AC: 21 AN: 320

Other (OTH) AF: 0.125 AC: 2 AN: 16

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

African (AFR) AF: 0.0961 AC: 3989 AN: 41524

American (AMR) AF: 0.176 AC: 2687 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.139 AC: 717 AN: 5154

South Asian (SAS) AF: 0.0737 AC: 355 AN: 4818

European-Finnish (FIN) AF: 0.0893 AC: 947 AN: 10600

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0942 AC: 6408 AN: 67998

Other (OTH) AF: 0.115 AC: 244 AN: 2116

Alfa AF: 0.0969 Hom.: 2125

Bravo AF: 0.112

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	7.5
DANN	Benign	0.73
PhyloP100		0.84
PromoterAI		-0.089	Neutral
Mutation Taster		=300/0	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: rs17522918; hg19: chr1-45987574;