rs7588627
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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
NM_012293.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.382
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]
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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 | UniProt |
---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.1568-19C>G | intron_variant | ENST00000252804.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXDN | ENST00000252804.9 | c.1568-19C>G | intron_variant | 1 | NM_012293.3 | P1 | |||
PXDN | ENST00000433670.5 | c.1555-19C>G | intron_variant | 1 | |||||
PXDN | ENST00000425171.2 | c.1496-19C>G | intron_variant | 5 | |||||
PXDN | ENST00000478155.5 | n.2160-19C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0747 AC: 11372AN: 152168Hom.: 1154 Cov.: 33
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GnomAD3 exomes AF: 0.0319 AC: 5540AN: 173914Hom.: 378 AF XY: 0.0274 AC XY: 2533AN XY: 92482
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GnomAD4 exome AF: 0.0139 AC: 19562AN: 1403890Hom.: 1330 Cov.: 28 AF XY: 0.0130 AC XY: 9023AN XY: 694528
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GnomAD4 genome ? AF: 0.0748 AC: 11392AN: 152286Hom.: 1157 Cov.: 33 AF XY: 0.0742 AC XY: 5529AN XY: 74472
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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 | PreventionGenetics, part of Exact Sciences | - | - - |
Anterior segment dysgenesis 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 18, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at