chr8-51502860-T-C

Position:

• chr8-51502860-T-C

Variant summary

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

The NM_144651.5(PXDNL):​c.381-3090A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,970 control chromosomes in the GnomAD database, including 18,431 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 0.47 (18431 hom., cov: 31)
• Consequence: PXDNL NM_144651.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PXDNL	NM_144651.5	c.381-3090A>G		intron_variant		ENST00000356297.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PXDNL	ENST00000356297.5	c.381-3090A>G		intron_variant		1	NM_144651.5	P1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71706 AN: 151852 Hom.: 18378 Cov.: 31

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.473 AC: 71827 AN: 151970 Hom.: 18431 Cov.: 31 AF XY: 0.476 AC XY: 35323 AN XY: 74250

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.478

Alfa AF: 0.392 Hom.: 22653

Bravo AF: 0.477

Asia WGS AF: 0.493 AC: 1715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs10755971; hg19: chr8-52415420;