rs1367819

Variant names:

• chr8-51455658-G-A
• rs1367819
• NM_144651.5:c.982+1840C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144651.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PXDNL	NM_144651.5	MANE Select	c.982+1840C>T		intron	N/A	NP_653252.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PXDNL	ENST00000356297.5	TSL:1 MANE Select	c.982+1840C>T		intron	N/A	ENSP00000348645.4	A1KZ92-1
	PXDNL	ENST00000894552.1		c.982+1840C>T		intron	N/A	ENSP00000564611.1
	PXDNL	ENST00000894549.1		c.910+1840C>T		intron	N/A	ENSP00000564608.1

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

African (AFR) AF: 0.699 AC: 28952 AN: 41444

American (AMR) AF: 0.317 AC: 4840 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3466

East Asian (EAS) AF: 0.358 AC: 1841 AN: 5142

South Asian (SAS) AF: 0.333 AC: 1600 AN: 4810

European-Finnish (FIN) AF: 0.357 AC: 3760 AN: 10536

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18941 AN: 67970

Other (OTH) AF: 0.417 AC: 881 AN: 2112

Alfa AF: 0.330 Hom.: 24588

Bravo AF: 0.421

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.082
DANN	Benign	0.40
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1367819; hg19: chr8-52368218;