rs718251

chr8-51801963-C-Achr8-51801963-C-T

Variant summary

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

The NM_144651.5(PXDNL):c.164+7218G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,968 control chromosomes in the GnomAD database, including 23,687 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 0.51 (23687 hom., cov: 31)
• Consequence: PXDNL NM_144651.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

PXDNL (HGNC:26359): (peroxidasin like) Predicted to enable heme binding activity and peroxidase activity. Predicted to be involved in hydrogen peroxide catabolic process. Predicted to be located in cytoplasm. Predicted to be active in extracellular space. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PXDNL	NM_144651.5	c.164+7218G>T		intron_variant		ENST00000356297.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PXDNL	ENST00000356297.5	c.164+7218G>T		intron_variant		1	NM_144651.5	P1

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77145 AN: 151850 Hom.: 23699 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.508 AC: 77134 AN: 151968 Hom.: 23687 Cov.: 31 AF XY: 0.505 AC XY: 37545 AN XY: 74274

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.533

Alfa AF: 0.631 Hom.: 19767

Bravo AF: 0.497

Asia WGS AF: 0.495 AC: 1724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.48
Dann	Benign	0.79

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: rs718251; hg19: chr8-52714523;