Variant rs7588627 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_012293.3(PXDN):c.1568-19C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0199 in 1,556,176 control chromosomes in the GnomAD database, including 2,487 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.075 ( 1157 hom., cov: 33)

Exomes 𝑓: 0.014 ( 1330 hom. )

Consequence

PXDN
NM_012293.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.382

Variant links:

Genes affected

PXDN (HGNC:14966): (peroxidasin) This gene encodes a heme-containing peroxidase that is secreted into the extracellular matrix. It is involved in extracellular matrix formation, and may function in the physiological and pathological fibrogenic response in fibrotic kidney. Mutations in this gene cause corneal opacification and other ocular anomalies, and also microphthalmia and anterior segment dysgenesis. [provided by RefSeq, Aug 2014]

PXDN links:

PXDN (HGNC:):

PXDN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 2-1662203-G-C is Benign according to our data. Variant chr2-1662203-G-C is described in ClinVar as [Benign]. Clinvar id is 260219.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PXDN	NM_012293.3 linkuse as main transcript	c.1568-19C>G		intron_variant		ENST00000252804.9	NP_036425.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
PXDN	ENST00000252804.9 linkuse as main transcript	c.1568-19C>G	intron_variant	1	NM_012293.3	ENSP00000252804.4	Q92626-1
PXDN	ENST00000433670.5 linkuse as main transcript	c.1553-19C>G	intron_variant	1		ENSP00000402738.1	H7C1W1
PXDN	ENST00000425171.2 linkuse as main transcript	c.1496-19C>G	intron_variant	5		ENSP00000398363.2	C9J4I9
PXDN	ENST00000478155.5 linkuse as main transcript	n.2160-19C>G	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0747

AC:

11372

AN:

152168

Hom.:

1154

Cov.:

show subpopulations

Gnomad AFR

AF:

0.228

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0277

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.0101

Gnomad FIN

AF:

0.0412

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00294

Gnomad OTH

AF:

0.0554

GnomAD3 exomes

AF:

0.0319

AC:

5540

AN:

173914

Hom.:

378

AF XY:

0.0274

AC XY:

2533

AN XY:

92482

show subpopulations

Gnomad AFR exome

AF:

0.235

Gnomad AMR exome

AF:

0.0136

Gnomad ASJ exome

AF:

0.0102

Gnomad EAS exome

AF:

0.125

Gnomad SAS exome

AF:

0.00607

Gnomad FIN exome

AF:

0.0430

Gnomad NFE exome

AF:

0.00306

Gnomad OTH exome

AF:

0.0248

GnomAD4 exome

AF:

0.0139

AC:

19562

AN:

1403890

Hom.:

1330

Cov.:

AF XY:

0.0130

AC XY:

9023

AN XY:

694528

show subpopulations

Gnomad4 AFR exome

AF:

0.241

Gnomad4 AMR exome

AF:

0.0148

Gnomad4 ASJ exome

AF:

0.0118

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.00714

Gnomad4 FIN exome

AF:

0.0404

Gnomad4 NFE exome

AF:

0.00230

Gnomad4 OTH exome

AF:

0.0296

GnomAD4 genome

AF:

0.0748

AC:

11392

AN:

152286

Hom.:

1157

Cov.:

AF XY:

0.0742

AC XY:

5529

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.228

Gnomad4 AMR

AF:

0.0276

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.00973

Gnomad4 FIN

AF:

0.0412

Gnomad4 NFE

AF:

0.00293

Gnomad4 OTH

AF:

0.0558

Alfa

AF:

0.0344

Hom.:

Bravo

AF:

0.0813

Asia WGS

AF:

0.0860

AC:

298

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 18, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Anterior segment dysgenesis 7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.45

DANN

Benign

0.29

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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