chr8-51806282-A-T

Position:

• chr8-51806282-A-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+2899T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,238 control chromosomes in the GnomAD database, including 61,623 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 0.89 (61623 hom., cov: 33)
• Consequence: PXDNL NM_144651.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

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]

PXDNL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PXDNL	NM_144651.5	c.164+2899T>A		intron_variant		ENST00000356297.5	NP_653252.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PXDNL	ENST00000356297.5	c.164+2899T>A		intron_variant		1	NM_144651.5	ENSP00000348645.4

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135141 AN: 152120 Hom.: 61606 Cov.: 33

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.888 AC: 135216 AN: 152238 Hom.: 61623 Cov.: 33 AF XY: 0.891 AC XY: 66342 AN XY: 74450

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.903

Alfa AF: 0.928 Hom.: 8275

Bravo AF: 0.877

Asia WGS AF: 0.938 AC: 3260 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.33

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: rs4242477; hg19: chr8-52718842;