chrX-23673144-G-A

Variant names:

• chrX-23673144-G-A
• rs528960
• NM_006406.2:c.359+1498G>A

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006406.2. 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
	PRDX4	NM_006406.2	MANE Select	c.359+1498G>A		intron	N/A	NP_006397.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX4	ENST00000379341.9	TSL:1 MANE Select	c.359+1498G>A		intron	N/A	ENSP00000368646.4
	PRDX4	ENST00000379331.3	TSL:2	c.359+1498G>A		intron	N/A	ENSP00000368635.3
	PRDX4	ENST00000379349.5	TSL:3	c.317+1498G>A		intron	N/A	ENSP00000368654.1

Frequencies

GnomAD3 genomes AF: 0.859 AC: 95218 AN: 110895 Hom.: 28772 Cov.: 23

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

African (AFR) AF: 0.740 AC: 22610 AN: 30563

American (AMR) AF: 0.867 AC: 9021 AN: 10401

Ashkenazi Jewish (ASJ) AF: 0.964 AC: 2542 AN: 2638

East Asian (EAS) AF: 0.945 AC: 3337 AN: 3530

South Asian (SAS) AF: 0.956 AC: 2524 AN: 2641

European-Finnish (FIN) AF: 0.925 AC: 5363 AN: 5796

Middle Eastern (MID) AF: 0.884 AC: 190 AN: 215

European-Non Finnish (NFE) AF: 0.901 AC: 47705 AN: 52968

Other (OTH) AF: 0.846 AC: 1280 AN: 1513

Alfa AF: 0.876 Hom.: 7634

Bravo AF: 0.847

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		0.069
Mutation Taster		=100/0	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: rs528960; hg19: chrX-23691261;