2-1635187-GT-G

Position:

• chr2-1635187-GT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_012293.3(PXDN):​c.4320+220del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,096 control chromosomes in the GnomAD database, including 5,199 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.25 (5199 hom., cov: 25)
• Consequence: PXDN NM_012293.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.308

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]

LOC124907723 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-1635187-GT-G is Benign according to our data. Variant chr2-1635187-GT-G is described in ClinVar as [Benign]. Clinvar id is 1252237.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PXDN	NM_012293.3	c.4320+220del		intron_variant		ENST00000252804.9	NP_036425.1
LOC124907723	XR_007086188.1	n.344-496del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PXDN	ENST00000252804.9	c.4320+220del		intron_variant		1	NM_012293.3	ENSP00000252804	P1
PXDN	ENST00000453308.1	c.*110+220del		intron_variant, NMD_transcript_variant		3		ENSP00000414098
PXDN	ENST00000478155.5	n.3408+220del		intron_variant, non_coding_transcript_variant		2
PXDN	ENST00000493654.1	n.1657+220del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38608 AN: 151978 Hom.: 5182 Cov.: 25

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.254 AC: 38661 AN: 152096 Hom.: 5199 Cov.: 25 AF XY: 0.262 AC XY: 19456 AN XY: 74346

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.251

Alfa AF: 0.229 Hom.: 505

Bravo AF: 0.262

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs11327409; hg19: chr2-1638959;