rs9425724

Variant names:

• chr1-173479361-A-G
• rs9425724
• NM_004905.3:c.95+1869A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004905.3(PRDX6):​c.95+1869A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,724 control chromosomes in the GnomAD database, including 12,217 homozygotes. 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 0.36 (12217 hom., cov: 32)
• Consequence: PRDX6 NM_004905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 3 publications found

Genes affected

PRDX6 (HGNC:16753): (peroxiredoxin 6) The protein encoded by this gene is a member of the thiol-specific antioxidant protein family. This protein is a bifunctional enzyme with two distinct active sites. It is involved in redox regulation of the cell; it can reduce H(2)O(2) and short chain organic, fatty acid, and phospholipid hydroperoxides. It may play a role in the regulation of phospholipid turnover as well as in protection against oxidative injury. [provided by RefSeq, Jul 2008]

PRDX6-AS1 (HGNC:54870): (PRDX6 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX6	NM_004905.3	c.95+1869A>G		intron_variant	Intron 1 of 4	ENST00000340385.6	NP_004896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX6	ENST00000340385.6	c.95+1869A>G		intron_variant	Intron 1 of 4	1	NM_004905.3	ENSP00000342026.5

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54376 AN: 151608 Hom.: 12166 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.359 AC: 54497 AN: 151724 Hom.: 12217 Cov.: 32 AF XY: 0.355 AC XY: 26325 AN XY: 74158

African (AFR) AF: 0.628 AC: 25888 AN: 41254

American (AMR) AF: 0.257 AC: 3932 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1175 AN: 3460

East Asian (EAS) AF: 0.592 AC: 3031 AN: 5122

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4826

European-Finnish (FIN) AF: 0.195 AC: 2058 AN: 10540

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16319 AN: 67936

Other (OTH) AF: 0.321 AC: 678 AN: 2110

Alfa AF: 0.323 Hom.: 1257

Bravo AF: 0.379

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.35
PhyloP100		-0.23
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: rs9425724; hg19: chr1-173448500;