rs2812968

chr10-34966173-A-Gchr10-34966173-A-T

Variant summary

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

The ENST00000451920.2(PRDX2P2):n.501A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 399,352 control chromosomes in the GnomAD database, including 49,002 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 0.52 (21276 hom., cov: 33)
  • Exomes 𝑓: 0.47 (27726 hom.)
• Consequence: PRDX2P2 ENST00000451920.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763

Genes affected

PRDX2P2 (HGNC:44967): (peroxiredoxin 2 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDX2P2	ENST00000451920.2	n.501A>G		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78293 AN: 151992 Hom.: 21234 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.483

GnomAD4 exome AF: 0.468 AC: 115680 AN: 247242 Hom.: 27726 Cov.: 0 AF XY: 0.464 AC XY: 66097 AN XY: 142522

Gnomad4 AFR exome AF: 0.700

Gnomad4 AMR exome AF: 0.517

Gnomad4 ASJ exome AF: 0.404

Gnomad4 EAS exome AF: 0.635

Gnomad4 SAS exome AF: 0.487

Gnomad4 FIN exome AF: 0.483

Gnomad4 NFE exome AF: 0.432

Gnomad4 OTH exome AF: 0.472

GnomAD4 genome AF: 0.515 AC: 78385 AN: 152110 Hom.: 21276 Cov.: 33 AF XY: 0.516 AC XY: 38386 AN XY: 74342

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.489

Alfa AF: 0.480 Hom.: 3750

Bravo AF: 0.525

Asia WGS AF: 0.617 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	1.7
Dann	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2812968; hg19: chr10-35255101;