chrX-23682356-G-A

Position:

• chrX-23682356-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_006406.2(PRDX4):​c.600-40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.60 (14284 hom., 18083 hem., cov: 20)
  • Exomes 𝑓: 0.58 (112004 hom. 160330 hem.)
  • Failed GnomAD Quality Control
• Consequence: PRDX4 NM_006406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

Genes affected

PRDX4 (HGNC:17169): (peroxiredoxin 4) The protein encoded by this gene is an antioxidant enzyme and belongs to the peroxiredoxin family. The protein is localized to the cytoplasm. Peroxidases of the peroxiredoxin family reduce hydrogen peroxide and alkyl hydroperoxides to water and alcohol with the use of reducing equivalents derived from thiol-containing donor molecules. This protein has been found to play a regulatory role in the activation of the transcription factor NF-kappaB. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRDX4	NM_006406.2	c.600-40G>A		intron_variant		ENST00000379341.9	NP_006397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDX4	ENST00000379341.9	c.600-40G>A		intron_variant		1	NM_006406.2	ENSP00000368646	P1
PRDX4	ENST00000439422.1	c.232-40G>A		intron_variant		3		ENSP00000413736

Frequencies

GnomAD3 genomes AF: 0.600 AC: 64846 AN: 108024 Hom.: 14285 Cov.: 20 AF XY: 0.594 AC XY: 18051 AN XY: 30376

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.602

GnomAD3 exomes AF: 0.602 AC: 84322 AN: 140013 Hom.: 19334 AF XY: 0.581 AC XY: 21968 AN XY: 37833

Gnomad AFR exome AF: 0.618

Gnomad AMR exome AF: 0.694

Gnomad ASJ exome AF: 0.712

Gnomad EAS exome AF: 0.746

Gnomad SAS exome AF: 0.572

Gnomad FIN exome AF: 0.523

Gnomad NFE exome AF: 0.564

Gnomad OTH exome AF: 0.594

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.577 AC: 544813 AN: 944921 Hom.: 112004 Cov.: 15 AF XY: 0.576 AC XY: 160330 AN XY: 278193

Gnomad4 AFR exome AF: 0.608

Gnomad4 AMR exome AF: 0.695

Gnomad4 ASJ exome AF: 0.730

Gnomad4 EAS exome AF: 0.736

Gnomad4 SAS exome AF: 0.584

Gnomad4 FIN exome AF: 0.524

Gnomad4 NFE exome AF: 0.565

Gnomad4 OTH exome AF: 0.593

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.600 AC: 64871 AN: 108081 Hom.: 14284 Cov.: 20 AF XY: 0.594 AC XY: 18083 AN XY: 30443

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.606

Alfa AF: 0.597 Hom.: 7373

Bravo AF: 0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.72

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: rs552105; hg19: chrX-23700473; COSMIC: COSV65025889; COSMIC: COSV65025889;