rs8735

Positions:

• chr10-80432957-T-A
• chr10-80432957-T-C
• chr10-80432957-T-G

Variant summary

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

The ENST00000606162.6(PRXL2A):​c.*858T>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 0.349 in 152,058 control chromosomes in the GnomAD database, including 10,991 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 0.35 (10991 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRXL2A ENST00000606162.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654

Genes affected

PRXL2A (HGNC:28651): (peroxiredoxin like 2A) Enables antioxidant activity. Involved in regulation of osteoclast differentiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRXL2A	NM_032333.5	c.*858T>A		3_prime_UTR_variant	6/6	ENST00000606162.6	NP_115709.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRXL2A	ENST00000606162.6	c.*858T>A		3_prime_UTR_variant	6/6	1	NM_032333.5	ENSP00000482445	P1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53044 AN: 151940 Hom.: 10988 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.386

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: 0.349 AC: 53049 AN: 152058 Hom.: 10991 Cov.: 32 AF XY: 0.355 AC XY: 26388 AN XY: 74352

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.385

Alfa AF: 0.226 Hom.: 585

Bravo AF: 0.342

Asia WGS AF: 0.497 AC: 1724 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8735; hg19: chr10-82192713;