NM_144651.5:c.164+2899T>A

Variant names:

• chr8-51806282-A-T
• rs4242477
• NM_144651.5:c.164+2899T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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.164+2899T>A		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.164+2899T>A		intron	N/A	ENSP00000348645.4
	PXDNL	ENST00000894552.1		c.164+2899T>A		intron	N/A	ENSP00000564611.1
	PXDNL	ENST00000894549.1		c.164+2899T>A		intron	N/A	ENSP00000564608.1

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

African (AFR) AF: 0.657 AC: 27278 AN: 41492

American (AMR) AF: 0.952 AC: 14555 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3331 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5163 AN: 5184

South Asian (SAS) AF: 0.944 AC: 4558 AN: 4826

European-Finnish (FIN) AF: 0.985 AC: 10462 AN: 10620

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66782 AN: 68034

Other (OTH) AF: 0.903 AC: 1910 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.33
PhyloP100		-0.31
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: rs4242477; hg19: chr8-52718842;