1-20068908-C-G

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229
Variant links:
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
PLA2G5XM_005245891.6 linkuse as main transcriptc.-42C>G 5_prime_UTR_variant 4/8 XP_005245948.1
PLA2G5XM_005245892.6 linkuse as main transcriptc.-42C>G 5_prime_UTR_variant 3/7 XP_005245949.1
PLA2G5XM_005245893.6 linkuse as main transcriptc.-307C>G 5_prime_UTR_variant 3/8 XP_005245950.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLA2G5ENST00000460175.5 linkuse as main transcriptn.373C>G non_coding_transcript_exon_variant 3/73
PLA2G5ENST00000465698.5 linkuse as main transcriptn.377C>G non_coding_transcript_exon_variant 3/83
PLA2G5ENST00000469069.5 linkuse as main transcriptn.400C>G non_coding_transcript_exon_variant 4/73

Frequencies

GnomAD3 genomes
AF:
0.000671
AC:
102
AN:
151940
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00235
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000180
AC:
24
AN:
133684
Hom.:
0
AF XY:
0.000137
AC XY:
10
AN XY:
72780
show subpopulations
Gnomad AFR exome
AF:
0.00202
Gnomad AMR exome
AF:
0.000205
Gnomad ASJ exome
AF:
0.000121
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000892
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000382
Gnomad OTH exome
AF:
0.000243
GnomAD4 exome
AF:
0.0000732
AC:
83
AN:
1133982
Hom.:
0
Cov.:
27
AF XY:
0.0000647
AC XY:
36
AN XY:
556532
show subpopulations
Gnomad4 AFR exome
AF:
0.00209
Gnomad4 AMR exome
AF:
0.000284
Gnomad4 ASJ exome
AF:
0.0000629
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000658
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000174
Gnomad4 OTH exome
AF:
0.0000483
GnomAD4 genome
AF:
0.000671
AC:
102
AN:
152058
Hom.:
0
Cov.:
31
AF XY:
0.000700
AC XY:
52
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.00234
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000194
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.66
DANN
Benign
0.56

Splicing

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: rs11573185; hg19: chr1-20395401; API