1-186861432-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024420.3(PLA2G4A):​c.33+7045C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,220 control chromosomes in the GnomAD database, including 56,904 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 0.86 ( 56904 hom., cov: 32)

Consequence

PLA2G4A
NM_024420.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.505
Variant links:
Genes affected
PLA2G4A (HGNC:9035): (phospholipase A2 group IVA) This gene encodes a member of the cytosolic phospholipase A2 group IV family. The enzyme catalyzes the hydrolysis of membrane phospholipids to release arachidonic acid which is subsequently metabolized into eicosanoids. Eicosanoids, including prostaglandins and leukotrienes, are lipid-based cellular hormones that regulate hemodynamics, inflammatory responses, and other intracellular pathways. The hydrolysis reaction also produces lysophospholipids that are converted into platelet-activating factor. The enzyme is activated by increased intracellular Ca(2+) levels and phosphorylation, resulting in its translocation from the cytosol and nucleus to perinuclear membrane vesicles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

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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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PLA2G4ANM_024420.3 linkc.33+7045C>T intron_variant Intron 2 of 17 ENST00000367466.4 NP_077734.2 P47712
PLA2G4ANM_001311193.2 linkc.33+7045C>T intron_variant Intron 2 of 15 NP_001298122.2 P47712B4DZI4
PLA2G4AXM_011509642.3 linkc.33+7045C>T intron_variant Intron 2 of 17 XP_011507944.1 P47712
PLA2G4AXM_047422599.1 linkc.33+7045C>T intron_variant Intron 2 of 14 XP_047278555.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PLA2G4AENST00000367466.4 linkc.33+7045C>T intron_variant Intron 2 of 17 1 NM_024420.3 ENSP00000356436.3 P47712
PLA2G4AENST00000466600.1 linkn.102+7045C>T intron_variant Intron 1 of 6 3

Frequencies

GnomAD3 genomes
AF:
0.862
AC:
131064
AN:
152102
Hom.:
56840
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.963
Gnomad AMI
AF:
0.701
Gnomad AMR
AF:
0.866
Gnomad ASJ
AF:
0.840
Gnomad EAS
AF:
0.788
Gnomad SAS
AF:
0.834
Gnomad FIN
AF:
0.780
Gnomad MID
AF:
0.848
Gnomad NFE
AF:
0.823
Gnomad OTH
AF:
0.858
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.862
AC:
131188
AN:
152220
Hom.:
56904
Cov.:
32
AF XY:
0.860
AC XY:
63994
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.963
Gnomad4 AMR
AF:
0.866
Gnomad4 ASJ
AF:
0.840
Gnomad4 EAS
AF:
0.788
Gnomad4 SAS
AF:
0.835
Gnomad4 FIN
AF:
0.780
Gnomad4 NFE
AF:
0.823
Gnomad4 OTH
AF:
0.859
Alfa
AF:
0.833
Hom.:
26340
Bravo
AF:
0.871
Asia WGS
AF:
0.827
AC:
2871
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.63
DANN
Benign
0.24

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10911933; hg19: chr1-186830564; API