rs528960

Positions:

• chrX-23673144-G-A
• chrX-23673144-G-C
• chrX-23673144-G-T

Variant summary

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

The NM_006406.2(PRDX4):​c.359+1498G>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 0.86 (28758 hom., 28626 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: PRDX4 NM_006406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDX4	NM_006406.2	c.359+1498G>A		intron_variant		ENST00000379341.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDX4	ENST00000379341.9	c.359+1498G>A		intron_variant		1	NM_006406.2	P1
PRDX4	ENST00000379331.3	c.359+1498G>A		intron_variant		2
PRDX4	ENST00000379349.5	c.317+1498G>A		intron_variant		3
PRDX4	ENST00000495599.1	n.471+1498G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.859 AC: 95218 AN: 110895 Hom.: 28772 Cov.: 23 AF XY: 0.864 AC XY: 28588 AN XY: 33101

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.925

Gnomad MID AF: 0.881

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.845

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.858 AC: 95236 AN: 110946 Hom.: 28758 Cov.: 23 AF XY: 0.863 AC XY: 28626 AN XY: 33162

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.964

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.956

Gnomad4 FIN AF: 0.925

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.846

Alfa AF: 0.876 Hom.: 7634

Bravo AF: 0.847

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.69

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: rs528960; hg19: chrX-23691261;