rs1367819

Positions:

• chr8-51455658-G-A
• chr8-51455658-G-C

Variant summary

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

The NM_144651.5(PXDNL):​c.982+1840C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,946 control chromosomes in the GnomAD database, including 15,435 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 0.41 (15435 hom., cov: 31)
• Consequence: PXDNL NM_144651.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PXDNL	NM_144651.5	c.982+1840C>T		intron_variant		ENST00000356297.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PXDNL	ENST00000356297.5	c.982+1840C>T		intron_variant		1	NM_144651.5	P1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62203 AN: 151828 Hom.: 15389 Cov.: 31

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.410 AC: 62313 AN: 151946 Hom.: 15435 Cov.: 31 AF XY: 0.410 AC XY: 30455 AN XY: 74268

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.417

Alfa AF: 0.301 Hom.: 10854

Bravo AF: 0.421

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.082
DANN	Benign	0.40

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: rs1367819; hg19: chr8-52368218;