rs2000

Positions:

• chr1-173488695-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_004905.3(PRDX6):​c.*832G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 152,326 control chromosomes in the GnomAD database, including 51 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 0.020 (51 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRDX6 NM_004905.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

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=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0204 (3113/152326) while in subpopulation NFE AF= 0.0317 (2155/68026). AF 95% confidence interval is 0.0306. There are 51 homozygotes in gnomad4. There are 1456 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 51 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDX6	NM_004905.3	c.*832G>A		3_prime_UTR_variant	5/5	ENST00000340385.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDX6	ENST00000340385.6	c.*832G>A		3_prime_UTR_variant	5/5	1	NM_004905.3	P1
PRDX6-AS1	ENST00000669220.1	n.117+596C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3117 AN: 152208 Hom.: 51 Cov.: 32

Gnomad AFR AF: 0.00564

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00972

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.0267

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0204 AC: 3113 AN: 152326 Hom.: 51 Cov.: 32 AF XY: 0.0195 AC XY: 1456 AN XY: 74496

Gnomad4 AFR AF: 0.00560

Gnomad4 AMR AF: 0.0227

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00973

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.0317

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0283 Hom.: 19

Bravo AF: 0.0209

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.43

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: rs2000; hg19: chr1-173457834;