rs2307276
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003706.3(PLA2G4C):c.1257+48C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 1,589,648 control chromosomes in the GnomAD database, including 1,419 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 0.055 ( 342 hom., cov: 31)
Exomes 𝑓: 0.034 ( 1077 hom. )
Consequence
PLA2G4C
NM_003706.3 intron
NM_003706.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.512
Genes affected
PLA2G4C (HGNC:9037): (phospholipase A2 group IVC) This gene encodes a protein which is a member of the phospholipase A2 enzyme family which hydrolyzes glycerophospholipids to produce free fatty acids and lysophospholipids, both of which serve as precursors in the production of signaling molecules. The encoded protein has been shown to be a calcium-independent and membrane bound enzyme. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G4C | NM_003706.3 | c.1257+48C>T | intron_variant | ENST00000599921.6 | |||
PLA2G4C-AS1 | NR_132363.1 | n.246G>A | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G4C | ENST00000599921.6 | c.1257+48C>T | intron_variant | 1 | NM_003706.3 | A2 | |||
PLA2G4C-AS1 | ENST00000596552.1 | n.189G>A | non_coding_transcript_exon_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0553 AC: 8398AN: 151976Hom.: 343 Cov.: 31
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GnomAD3 exomes AF: 0.0329 AC: 7987AN: 242532Hom.: 245 AF XY: 0.0314 AC XY: 4129AN XY: 131486
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GnomAD4 exome AF: 0.0342 AC: 49167AN: 1437554Hom.: 1077 Cov.: 27 AF XY: 0.0334 AC XY: 23917AN XY: 715850
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GnomAD4 genome ? AF: 0.0553 AC: 8408AN: 152094Hom.: 342 Cov.: 31 AF XY: 0.0532 AC XY: 3957AN XY: 74344
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ClinVar
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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at