rs76863441
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005084.4(PLA2G7):c.835G>T(p.Val279Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,607,748 control chromosomes in the GnomAD database, including 399 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005084.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLA2G7 | ENST00000274793.12 | c.835G>T | p.Val279Phe | missense_variant | Exon 9 of 12 | 1 | NM_005084.4 | ENSP00000274793.7 | ||
PLA2G7 | ENST00000537365.1 | c.835G>T | p.Val279Phe | missense_variant | Exon 9 of 12 | 1 | ENSP00000445666.1 |
Frequencies
GnomAD3 genomes AF: 0.00268 AC: 408AN: 152092Hom.: 21 Cov.: 32
GnomAD3 exomes AF: 0.00455 AC: 1141AN: 251010Hom.: 40 AF XY: 0.00425 AC XY: 576AN XY: 135680
GnomAD4 exome AF: 0.00362 AC: 5270AN: 1455538Hom.: 378 Cov.: 27 AF XY: 0.00354 AC XY: 2562AN XY: 724626
GnomAD4 genome AF: 0.00267 AC: 406AN: 152210Hom.: 21 Cov.: 32 AF XY: 0.00308 AC XY: 229AN XY: 74418
ClinVar
Submissions by phenotype
Platelet-activating factor acetylhydrolase deficiency Pathogenic:1Other:1
- -
NM_005084.3:c.835G>T in the PLA2G7 gene has an allele frequency of 0.056 in East Asian subpopulation in the gnomAD database, including 41 homozygous occurrences. This variant has been reported as a genetic risk factor for stroke, asthma and cardiovascular disease (PMID: 9412624, 10194471, 16787988). Taken together, we interprete this variant as risk factor variant. -
PLA2G7-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
This variant is associated with the following publications: (PMID: 21834908, 19373214, 20080080, 20185515, 19034521, 9472966, 21606947, 21490708, 20926117, 16086290, 8675689, 11916011, 10194471, 9759612, 9412624, 16787988, 26595893, 26791069, 31589614, 11248283) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at