X-23682576-A-T

Variant names:

• chrX-23682576-A-T
• rs795489
• NM_006406.2:c.730+50A>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_006406.2(PRDX4):​c.730+50A>T 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: not found (cov: 20)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: PRDX4 NM_006406.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 10 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=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX4	NM_006406.2	c.730+50A>T		intron_variant	Intron 5 of 6	ENST00000379341.9	NP_006397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX4	ENST00000379341.9	c.730+50A>T		intron_variant	Intron 5 of 6	1	NM_006406.2	ENSP00000368646.4
PRDX4	ENST00000439422.1	c.361+50A>T		intron_variant	Intron 3 of 5	3		ENSP00000413736.1

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 887894 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 237268

African (AFR) AF: 0.00 AC: 0 AN: 20006

American (AMR) AF: 0.00 AC: 0 AN: 20871

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13724

East Asian (EAS) AF: 0.00 AC: 0 AN: 22251

South Asian (SAS) AF: 0.00 AC: 0 AN: 37485

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32712

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3365

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 701355

Other (OTH) AF: 0.00 AC: 0 AN: 36125

GnomAD4 genome Cov.: 20

Alfa AF: 0.00 Hom.: 11199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.68
PhyloP100		1.3

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: rs795489; hg19: chrX-23700693;