chr1-45517172-A-G

Position:

• chr1-45517172-A-G

Variant summary

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

The NM_181697.3(PRDX1):​c.107-1365T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,960 control chromosomes in the GnomAD database, including 41,801 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 0.74 (41801 hom., cov: 30)
• Consequence: PRDX1 NM_181697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDX1	NM_181697.3	c.107-1365T>C		intron_variant		ENST00000319248.13
PRDX1	NM_001202431.2	c.107-1365T>C		intron_variant
PRDX1	NM_002574.4	c.107-1365T>C		intron_variant
PRDX1	NM_181696.3	c.107-1365T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDX1	ENST00000319248.13	c.107-1365T>C		intron_variant		1	NM_181697.3	P1

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112026 AN: 151842 Hom.: 41772 Cov.: 30

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.736

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.738 AC: 112107 AN: 151960 Hom.: 41801 Cov.: 30 AF XY: 0.742 AC XY: 55108 AN XY: 74250

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.738

Alfa AF: 0.685 Hom.: 5763

Bravo AF: 0.750

Asia WGS AF: 0.857 AC: 2977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.8
DANN	Benign	0.78

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: rs6667191; hg19: chr1-45982844;