rs7540065

Variant names:

• chr1-173479897-G-A
• rs7540065
• NM_004905.3:c.96-1429G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004905.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX6	NM_004905.3	MANE Select	c.96-1429G>A		intron	N/A	NP_004896.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX6	ENST00000340385.6	TSL:1 MANE Select	c.96-1429G>A		intron	N/A	ENSP00000342026.5
	PRDX6	ENST00000460950.1	TSL:2	n.164-1429G>A		intron	N/A
	PRDX6-AS1	ENST00000669220.1		n.117+9394C>T		intron	N/A

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

African (AFR) AF: 0.633 AC: 26240 AN: 41424

American (AMR) AF: 0.260 AC: 3973 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1184 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3077 AN: 5152

South Asian (SAS) AF: 0.222 AC: 1073 AN: 4828

European-Finnish (FIN) AF: 0.197 AC: 2088 AN: 10574

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16422 AN: 67994

Other (OTH) AF: 0.323 AC: 682 AN: 2112

Alfa AF: 0.269 Hom.: 3693

Bravo AF: 0.381

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.28
DANN	Benign	0.82
PhyloP100		-1.1
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: rs7540065; hg19: chr1-173449036;