rs7314

Variant names:

• chr1-173488460-A-G
• rs7314
• NM_004905.3:c.*597A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-173488460-A-G
• chr1-173488460-A-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.*597A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,144 control chromosomes in the GnomAD database, including 12,458 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 (12458 hom., cov: 32)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: PRDX6 NM_004905.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 20 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX6	NM_004905.3	c.*597A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000340385.6	NP_004896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX6	ENST00000340385.6	c.*597A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_004905.3	ENSP00000342026.5
PRDX6-AS1	ENST00000669220.1	n.117+831T>C		intron_variant	Intron 1 of 3
PRDX6-AS1	ENST00000778745.1	n.112+831T>C		intron_variant	Intron 1 of 2
PRDX6-AS1	ENST00000778747.1	n.114+831T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54868 AN: 152012 Hom.: 12404 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.321

GnomAD4 exome AF: 0.143 AC: 2 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.0833 AC XY: 1 AN XY: 12

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) AF: 0.143 AC: 2 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.361 AC: 54994 AN: 152130 Hom.: 12458 Cov.: 32 AF XY: 0.357 AC XY: 26552 AN XY: 74370

African (AFR) AF: 0.630 AC: 26152 AN: 41484

American (AMR) AF: 0.259 AC: 3954 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3085 AN: 5170

South Asian (SAS) AF: 0.222 AC: 1069 AN: 4826

European-Finnish (FIN) AF: 0.198 AC: 2093 AN: 10592

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

European-Non Finnish (NFE) AF: 0.242 AC: 16425 AN: 67996

Other (OTH) AF: 0.324 AC: 683 AN: 2110

Alfa AF: 0.280 Hom.: 16820

Bravo AF: 0.380

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.86
PhyloP100		-0.059
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: rs7314; hg19: chr1-173457599;