rs2285714
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_030821.5(PLA2G12A):c.345G>A(p.Glu115=) variant causes a synonymous change. The variant allele was found at a frequency of 0.402 in 1,613,256 control chromosomes in the GnomAD database, including 136,736 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 0.31 ( 9095 hom., cov: 32)
Exomes 𝑓: 0.41 ( 127641 hom. )
Consequence
PLA2G12A
NM_030821.5 synonymous
NM_030821.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.12
Genes affected
PLA2G12A (HGNC:18554): (phospholipase A2 group XIIA) Secreted phospholipase A2 (sPLA2) enzymes liberate arachidonic acid from phospholipids for production of eicosanoids and exert a variety of physiologic and pathologic effects. Group XII sPLA2s, such as PLA2G12A, have relatively low specific activity and are structurally and functionally distinct from other sPLA2s (Gelb et al., 2000 [PubMed 11031251]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.2).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G12A | NM_030821.5 | c.345G>A | p.Glu115= | synonymous_variant | 3/4 | ENST00000243501.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G12A | ENST00000243501.10 | c.345G>A | p.Glu115= | synonymous_variant | 3/4 | 1 | NM_030821.5 | P3 | |
PLA2G12A | ENST00000502283.1 | c.339G>A | p.Glu113= | synonymous_variant | 3/4 | 1 | A1 | ||
PLA2G12A | ENST00000502772.1 | n.139G>A | non_coding_transcript_exon_variant | 2/2 | 5 | ||||
PLA2G12A | ENST00000507961.1 | c.*55G>A | 3_prime_UTR_variant, NMD_transcript_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.312 AC: 47374AN: 151968Hom.: 9095 Cov.: 32
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GnomAD3 exomes AF: 0.374 AC: 94001AN: 251360Hom.: 18909 AF XY: 0.380 AC XY: 51580AN XY: 135858
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GnomAD4 exome AF: 0.412 AC: 601509AN: 1461168Hom.: 127641 Cov.: 41 AF XY: 0.411 AC XY: 298976AN XY: 726910
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GnomAD4 genome ? AF: 0.312 AC: 47377AN: 152088Hom.: 9095 Cov.: 32 AF XY: 0.310 AC XY: 23062AN XY: 74326
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Not reported inComputational scores
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Name
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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