rs9395208
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000537365.1(PLA2G7):c.-67C>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 0.205 in 152,576 control chromosomes in the GnomAD database, including 3,556 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 0.21 ( 3548 hom., cov: 33)
Exomes 𝑓: 0.20 ( 8 hom. )
Consequence
PLA2G7
ENST00000537365.1 5_prime_UTR
ENST00000537365.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.45
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G7 | NM_001168357.2 | c.-67C>G | 5_prime_UTR_variant | 1/12 | |||
PLA2G7 | XM_005249408.5 | c.-35+36C>G | intron_variant | ||||
PLA2G7 | XM_047419359.1 | c.-27+36C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G7 | ENST00000537365.1 | c.-67C>G | 5_prime_UTR_variant | 1/12 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.205 AC: 31231AN: 152164Hom.: 3540 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
31231
AN:
152164
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.204 AC: 60AN: 294Hom.: 8 Cov.: 0 AF XY: 0.212 AC XY: 44AN XY: 208
GnomAD4 exome
AF:
AC:
60
AN:
294
Hom.:
Cov.:
0
AF XY:
AC XY:
44
AN XY:
208
Gnomad4 AFR exome
AF:
Gnomad4 AMR 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: 0.205 AC: 31262AN: 152282Hom.: 3548 Cov.: 33 AF XY: 0.212 AC XY: 15814AN XY: 74444
GnomAD4 genome
?
AF:
AC:
31262
AN:
152282
Hom.:
Cov.:
33
AF XY:
AC XY:
15814
AN XY:
74444
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1141
AN:
3478
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