rs77999529

chr10-80416446-G-C

Variant summary

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

The NM_032333.5(PRXL2A):c.-2-4020G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0294 in 152,214 control chromosomes in the GnomAD database, including 153 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 0.029 (153 hom., cov: 33)
• Consequence: PRXL2A NM_032333.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRXL2A	NM_032333.5	c.-2-4020G>C		intron_variant		ENST00000606162.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRXL2A	ENST00000606162.6	c.-2-4020G>C		intron_variant		1	NM_032333.5	P1

Frequencies

GnomAD3 genomes AF: 0.0293 AC: 4464 AN: 152096 Hom.: 151 Cov.: 33

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0319

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00282

Gnomad OTH AF: 0.0279

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0294 AC: 4482 AN: 152214 Hom.: 153 Cov.: 33 AF XY: 0.0328 AC XY: 2444 AN XY: 74404

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.0194

Gnomad4 ASJ AF: 0.00835

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0319

Gnomad4 NFE AF: 0.00282

Gnomad4 OTH AF: 0.0314

Alfa AF: 0.0168 Hom.: 10

Bravo AF: 0.0264

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.1
Dann	Benign	0.71

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: rs77999529; hg19: chr10-82176202;