X-23683293-A-C

Position:

• chrX-23683293-A-C

Variant summary

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

The NM_006406.2(PRDX4):​c.731-378A>C 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 (14322 hom., 19402 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: PRDX4 NM_006406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDX4	NM_006406.2	c.731-378A>C		intron_variant		ENST00000379341.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDX4	ENST00000379341.9	c.731-378A>C		intron_variant		1	NM_006406.2	P1
PRDX4	ENST00000439422.1	c.363-378A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.602 AC: 66248 AN: 110112 Hom.: 14323 Cov.: 22 AF XY: 0.598 AC XY: 19368 AN XY: 32378

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.605

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: 0.602 AC: 66275 AN: 110168 Hom.: 14322 Cov.: 22 AF XY: 0.598 AC XY: 19402 AN XY: 32444

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.609

Alfa AF: 0.568 Hom.: 4069

Bravo AF: 0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.34

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: rs1548734; hg19: chrX-23701410;