rs1548734

Variant names:

• chrX-23683293-A-C
• rs1548734
• NM_006406.2:c.731-378A>C

Your query was ambiguous. Multiple possible variants found:

• chrX-23683293-A-C
• chrX-23683293-A-G
• chrX-23683293-A-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.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
• Publications: 2 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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX4	NM_006406.2	c.731-378A>C		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.731-378A>C		intron_variant	Intron 5 of 6	1	NM_006406.2	ENSP00000368646.4
PRDX4	ENST00000439422.1	c.362-378A>C		intron_variant	Intron 3 of 5	3		ENSP00000413736.1

Frequencies

GnomAD3 genomes AF: 0.602 AC: 66248 AN: 110112 Hom.: 14323 Cov.: 22

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

African (AFR) AF: 0.617 AC: 18721 AN: 30334

American (AMR) AF: 0.673 AC: 6869 AN: 10201

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 1927 AN: 2634

East Asian (EAS) AF: 0.745 AC: 2591 AN: 3479

South Asian (SAS) AF: 0.590 AC: 1541 AN: 2614

European-Finnish (FIN) AF: 0.514 AC: 2975 AN: 5787

Middle Eastern (MID) AF: 0.696 AC: 149 AN: 214

European-Non Finnish (NFE) AF: 0.571 AC: 30099 AN: 52732

Other (OTH) AF: 0.609 AC: 919 AN: 1508

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
PhyloP100		-1.3
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: rs1548734; hg19: chrX-23701410;