rs7540065

Positions:

• chr1-173479897-G-A
• chr1-173479897-G-C
• chr1-173479897-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004905.3(PRDX6):​c.96-1429G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,044 control chromosomes in the GnomAD database, including 12,513 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 (12513 hom., cov: 32)
• Consequence: PRDX6 NM_004905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRDX6	NM_004905.3	c.96-1429G>A		intron_variant		ENST00000340385.6	NP_004896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDX6	ENST00000340385.6	c.96-1429G>A		intron_variant		1	NM_004905.3	ENSP00000342026	P1
PRDX6-AS1	ENST00000669220.1	n.117+9394C>T		intron_variant, non_coding_transcript_variant
PRDX6	ENST00000460950.1	n.164-1429G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54966 AN: 151926 Hom.: 12460 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.362 AC: 55091 AN: 152044 Hom.: 12513 Cov.: 32 AF XY: 0.358 AC XY: 26606 AN XY: 74330

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.323

Alfa AF: 0.265 Hom.: 3211

Bravo AF: 0.381

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	-0.85
CADD	Benign	0.28
DANN	Benign	0.82

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: rs7540065; hg19: chr1-173449036;