rs1554182722
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_005084.4(PLA2G7):c.680_681dupAA(p.Glu228LysfsTer9) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,736 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
PLA2G7
NM_005084.4 frameshift
NM_005084.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.321
Publications
0 publications found
Genes affected
PLA2G7 (HGNC:9040): (phospholipase A2 group VII) The protein encoded by this gene is a secreted enzyme that catalyzes the degradation of platelet-activating factor to biologically inactive products. Defects in this gene are a cause of platelet-activating factor acetylhydrolase deficiency. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Dec 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PLA2G7 | NM_005084.4 | c.680_681dupAA | p.Glu228LysfsTer9 | frameshift_variant | Exon 8 of 12 | ENST00000274793.12 | NP_005075.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PLA2G7 | ENST00000274793.12 | c.680_681dupAA | p.Glu228LysfsTer9 | frameshift_variant | Exon 8 of 12 | 1 | NM_005084.4 | ENSP00000274793.7 | ||
| PLA2G7 | ENST00000537365.1 | c.680_681dupAA | p.Glu228LysfsTer9 | frameshift_variant | Exon 8 of 12 | 1 | ENSP00000445666.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459736Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 726406 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1459736
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
726406
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33418
American (AMR)
AF:
AC:
0
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26112
East Asian (EAS)
AF:
AC:
0
AN:
39662
South Asian (SAS)
AF:
AC:
0
AN:
86226
European-Finnish (FIN)
AF:
AC:
0
AN:
53364
Middle Eastern (MID)
AF:
AC:
0
AN:
5762
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1110136
Other (OTH)
AF:
AC:
0
AN:
60336
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.600
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Platelet-activating factor acetylhydrolase deficiency Uncertain:1
Mar 05, 2018
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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