Variant rs7837348 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_144651.5(PXDNL):c.486A>G(p.Pro162Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 1,510,642 control chromosomes in the GnomAD database, including 25,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 5145 hom., cov: 33)

Exomes 𝑓: 0.16 ( 20207 hom. )

Consequence

PXDNL
NM_144651.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.48

Variant links:

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 links:

PXDNL (HGNC:):

PXDNL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 8-51483681-T-C is Benign according to our data. Variant chr8-51483681-T-C is described in ClinVar as [Benign]. Clinvar id is 403358.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PXDNL	NM_144651.5 linkuse as main transcript	c.486A>G	p.Pro162Pro	synonymous_variant	6/23	ENST00000356297.5	NP_653252.4	A1KZ92-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PXDNL	ENST00000356297.5 linkuse as main transcript	c.486A>G	p.Pro162Pro	synonymous_variant	6/23	1	NM_144651.5	ENSP00000348645.4		A1KZ92-1

Frequencies

GnomAD3 genomes

AF:

0.236

AC:

35925

AN:

152018

Hom.:

5124

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.0591

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.227

GnomAD3 exomes

AF:

0.183

AC:

27691

AN:

151224

Hom.:

2899

AF XY:

0.180

AC XY:

14388

AN XY:

79840

show subpopulations

Gnomad AFR exome

AF:

0.403

Gnomad AMR exome

AF:

0.216

Gnomad ASJ exome

AF:

0.127

Gnomad EAS exome

AF:

0.0586

Gnomad SAS exome

AF:

0.198

Gnomad FIN exome

AF:

0.192

Gnomad NFE exome

AF:

0.164

Gnomad OTH exome

AF:

0.170

GnomAD4 exome

AF:

0.164

AC:

222576

AN:

1358506

Hom.:

20207

Cov.:

AF XY:

0.165

AC XY:

110906

AN XY:

671748

show subpopulations

Gnomad4 AFR exome

AF:

0.396

Gnomad4 AMR exome

AF:

0.219

Gnomad4 ASJ exome

AF:

0.127

Gnomad4 EAS exome

AF:

0.0594

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.188

Gnomad4 NFE exome

AF:

0.155

Gnomad4 OTH exome

AF:

0.175

GnomAD4 genome

AF:

0.237

AC:

36006

AN:

152136

Hom.:

5145

Cov.:

AF XY:

0.237

AC XY:

17655

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.399

Gnomad4 AMR

AF:

0.238

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.0592

Gnomad4 SAS

AF:

0.202

Gnomad4 FIN

AF:

0.193

Gnomad4 NFE

AF:

0.168

Gnomad4 OTH

AF:

0.228

Alfa

AF:

0.193

Hom.:

1945

Bravo

AF:

0.243

Asia WGS

AF:

0.188

AC:

656

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

PXDNL-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 05, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.8

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over