rs2307246
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001395463.1(PLA2G2A):c.185+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 1,608,878 control chromosomes in the GnomAD database, including 36,779 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 0.18 ( 2800 hom., cov: 32)
Exomes 𝑓: 0.21 ( 33979 hom. )
Consequence
PLA2G2A
NM_001395463.1 intron
NM_001395463.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.284
Genes affected
PLA2G2A (HGNC:9031): (phospholipase A2 group IIA) The protein encoded by this gene is a member of the phospholipase A2 family (PLA2). PLA2s constitute a diverse family of enzymes with respect to sequence, function, localization, and divalent cation requirements. This gene product belongs to group II, which contains secreted form of PLA2, an extracellular enzyme that has a low molecular mass and requires calcium ions for catalysis. It catalyzes the hydrolysis of the sn-2 fatty acid acyl ester bond of phosphoglycerides, releasing free fatty acids and lysophospholipids, and thought to participate in the regulation of the phospholipid metabolism in biomembranes. Several alternatively spliced transcript variants with different 5' UTRs have been found for this gene.[provided by RefSeq, Sep 2009]
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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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLA2G2A | NM_001395463.1 | c.185+16C>T | intron_variant | ENST00000482011.3 | NP_001382392.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLA2G2A | ENST00000482011.3 | c.185+16C>T | intron_variant | 1 | NM_001395463.1 | ENSP00000504762.1 |
Frequencies
GnomAD3 genomes AF: 0.176 AC: 26736AN: 152064Hom.: 2795 Cov.: 32
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GnomAD3 exomes AF: 0.175 AC: 43559AN: 248664Hom.: 4599 AF XY: 0.177 AC XY: 23868AN XY: 134518
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GnomAD4 exome AF: 0.208 AC: 303597AN: 1456696Hom.: 33979 Cov.: 34 AF XY: 0.207 AC XY: 149821AN XY: 724520
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GnomAD4 genome AF: 0.176 AC: 26757AN: 152182Hom.: 2800 Cov.: 32 AF XY: 0.173 AC XY: 12900AN XY: 74410
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at