chr1-20082881-A-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000929.3(PLA2G5):​c.-10-1940A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,818 control chromosomes in the GnomAD database, including 23,782 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 0.56 ( 23782 hom., cov: 33)

Consequence

PLA2G5
NM_000929.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.115

Publications

9 publications found
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]
PLA2G5 Gene-Disease associations (from GenCC):
  • familial benign flecked retina
    Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE, LIMITED Submitted by: G2P, Ambry Genetics, Orphanet
  • late-adult onset retinitis pigmentosa
    Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PLA2G5NM_000929.3 linkc.-10-1940A>C intron_variant Intron 1 of 4 ENST00000375108.4 NP_000920.1 P39877

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PLA2G5ENST00000375108.4 linkc.-10-1940A>C intron_variant Intron 1 of 4 1 NM_000929.3 ENSP00000364249.3 P39877

Frequencies

GnomAD3 genomes
AF:
0.555
AC:
84165
AN:
151698
Hom.:
23737
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.515
Gnomad AMI
AF:
0.652
Gnomad AMR
AF:
0.606
Gnomad ASJ
AF:
0.651
Gnomad EAS
AF:
0.574
Gnomad SAS
AF:
0.547
Gnomad FIN
AF:
0.556
Gnomad MID
AF:
0.712
Gnomad NFE
AF:
0.558
Gnomad OTH
AF:
0.596
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.555
AC:
84274
AN:
151818
Hom.:
23782
Cov.:
33
AF XY:
0.557
AC XY:
41327
AN XY:
74244
show subpopulations
African (AFR)
AF:
0.516
AC:
21233
AN:
41166
American (AMR)
AF:
0.606
AC:
9253
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.651
AC:
2261
AN:
3472
East Asian (EAS)
AF:
0.575
AC:
2973
AN:
5172
South Asian (SAS)
AF:
0.550
AC:
2652
AN:
4826
European-Finnish (FIN)
AF:
0.556
AC:
5877
AN:
10578
Middle Eastern (MID)
AF:
0.701
AC:
206
AN:
294
European-Non Finnish (NFE)
AF:
0.558
AC:
37965
AN:
68010
Other (OTH)
AF:
0.598
AC:
1261
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1961
3923
5884
7846
9807
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
730
1460
2190
2920
3650
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.559
Hom.:
32810
Bravo
AF:
0.555
Asia WGS
AF:
0.589
AC:
2047
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
7.0
DANN
Benign
0.63
PhyloP100
0.12
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs525380; hg19: chr1-20409374; API