1-173488695-G-A

Variant names:

• chr1-173488695-G-A
• rs2000
• NM_004905.3:c.*832G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 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)

LOC124904456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 51 AR gene

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.*832G>A		3_prime_UTR	Exon 5 of 5	NP_004896.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX6	ENST00000340385.6	TSL:1 MANE Select	c.*832G>A		3_prime_UTR	Exon 5 of 5	ENSP00000342026.5
	PRDX6-AS1	ENST00000669220.1		n.117+596C>T		intron	N/A
	PRDX6-AS1	ENST00000778745.1		n.112+596C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.00560 AC: 233 AN: 41576

American (AMR) AF: 0.0227 AC: 348 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.00973 AC: 47 AN: 4830

European-Finnish (FIN) AF: 0.0111 AC: 118 AN: 10618

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0317 AC: 2155 AN: 68026

Other (OTH) AF: 0.0260 AC: 55 AN: 2116

Alfa AF: 0.0282 Hom.: 21

Bravo AF: 0.0209

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.43
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism

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: rs2000; hg19: chr1-173457834;