1-20068908-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The XM_005245891.6(PLA2G5):c.-42C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,286,040 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00067 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000073 ( 0 hom. )
Consequence
PLA2G5
XM_005245891.6 5_prime_UTR
XM_005245891.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.229
Genes affected
PLA2G5 (HGNC:9038): (phospholipase A2 group V) This gene is a member of the secretory phospholipase A2 family. It is located in a tightly-linked cluster of secretory phospholipase A2 genes on chromosome 1. The encoded enzyme catalyzes the hydrolysis of membrane phospholipids to generate lysophospholipids and free fatty acids including arachidonic acid. It preferentially hydrolyzes linoleoyl-containing phosphatidylcholine substrates. Secretion of this enzyme is thought to induce inflammatory responses in neighboring cells. Alternatively spliced transcript variants have been found, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLA2G5 | XM_005245891.6 | c.-42C>G | 5_prime_UTR_variant | 4/8 | XP_005245948.1 | |||
PLA2G5 | XM_005245892.6 | c.-42C>G | 5_prime_UTR_variant | 3/7 | XP_005245949.1 | |||
PLA2G5 | XM_005245893.6 | c.-307C>G | 5_prime_UTR_variant | 3/8 | XP_005245950.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLA2G5 | ENST00000460175.5 | n.373C>G | non_coding_transcript_exon_variant | 3/7 | 3 | |||||
PLA2G5 | ENST00000465698.5 | n.377C>G | non_coding_transcript_exon_variant | 3/8 | 3 | |||||
PLA2G5 | ENST00000469069.5 | n.400C>G | non_coding_transcript_exon_variant | 4/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000671 AC: 102AN: 151940Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
102
AN:
151940
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000180 AC: 24AN: 133684Hom.: 0 AF XY: 0.000137 AC XY: 10AN XY: 72780
GnomAD3 exomes
AF:
AC:
24
AN:
133684
Hom.:
AF XY:
AC XY:
10
AN XY:
72780
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000732 AC: 83AN: 1133982Hom.: 0 Cov.: 27 AF XY: 0.0000647 AC XY: 36AN XY: 556532
GnomAD4 exome
AF:
AC:
83
AN:
1133982
Hom.:
Cov.:
27
AF XY:
AC XY:
36
AN XY:
556532
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000671 AC: 102AN: 152058Hom.: 0 Cov.: 31 AF XY: 0.000700 AC XY: 52AN XY: 74310
GnomAD4 genome
AF:
AC:
102
AN:
152058
Hom.:
Cov.:
31
AF XY:
AC XY:
52
AN XY:
74310
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at