rs1058440
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007366.5(PLA2R1):c.2183+72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 741,284 control chromosomes in the GnomAD database, including 770 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 0.047 ( 104 hom., cov: 26)
Exomes 𝑓: 0.040 ( 666 hom. )
Consequence
PLA2R1
NM_007366.5 intron
NM_007366.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.467
Genes affected
PLA2R1 (HGNC:9042): (phospholipase A2 receptor 1) This gene represents a phospholipase A2 receptor. The encoded protein likely exists as both a transmembrane form and a soluble form. The transmembrane receptor may play a role in clearance of phospholipase A2, thereby inhibiting its action. Polymorphisms at this locus have been associated with susceptibility to idiopathic membranous nephropathy. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0934 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2R1 | NM_007366.5 | c.2183+72G>A | intron_variant | ENST00000283243.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2R1 | ENST00000283243.13 | c.2183+72G>A | intron_variant | 1 | NM_007366.5 | P1 | |||
PLA2R1 | ENST00000392771.1 | c.2183+72G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0471 AC: 4375AN: 92902Hom.: 104 Cov.: 26
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GnomAD4 exome AF: 0.0396 AC: 25685AN: 648272Hom.: 666 AF XY: 0.0401 AC XY: 13559AN XY: 337728
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GnomAD4 genome ? AF: 0.0470 AC: 4372AN: 93012Hom.: 104 Cov.: 26 AF XY: 0.0466 AC XY: 2111AN XY: 45340
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ClinVar
Not reported inComputational 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