6-46711495-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 9P and 4B. PVS1PP3BS2
The NM_005084.4(PLA2G7):c.663+1G>A variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000406 in 1,613,580 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005084.4 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLA2G7 | ENST00000274793.12 | c.663+1G>A | splice_donor_variant, intron_variant | Intron 7 of 11 | 1 | NM_005084.4 | ENSP00000274793.7 | |||
PLA2G7 | ENST00000537365.1 | c.663+1G>A | splice_donor_variant, intron_variant | Intron 7 of 11 | 1 | ENSP00000445666.1 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000963 AC: 242AN: 251324Hom.: 3 AF XY: 0.00120 AC XY: 163AN XY: 135838
GnomAD4 exome AF: 0.000417 AC: 610AN: 1461312Hom.: 8 Cov.: 31 AF XY: 0.000596 AC XY: 433AN XY: 726968
GnomAD4 genome AF: 0.000296 AC: 45AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000457 AC XY: 34AN XY: 74456
ClinVar
Submissions by phenotype
Platelet-activating factor acetylhydrolase deficiency Pathogenic:1Other:1
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NG_016204.1(NM_001168357.1):c.663+1G>A in the PLA2G7 gene has an allele frequency of 0.008 in South Asian subpopulation in the gnomAD database, including three homozygotes. The c.663+1G>A variant destroys the canonical splice donor site in intron 13. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product if the message is used for protein translation. However, activity of soluble lipoprotein-associated phospholipase A2 (encoded by PLA2G7) has been correlated with risk for coronary heart disease (PMID: 28406212). Taken together, we interprete this variant as risk factor variant. -
not specified Uncertain:1
Variant summary: PLA2G7 c.663+1G>A alters a conserved nucleotide located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00096 in 251324 control chromosomes in the gnomAD database, including 3 homozygotes. This frequency does not allow conclusions about variant significance. c.663+1G>A has been reported in the literature in individuals affected with Lipoprotein-associated phospholipase A2 (Lp-PLA2) Deficiency, an enzyme that hydrolyzes phospholipids to generate lysophosphatidylcholine and oxidized nonesterified fatty acids (example, Salaheen_2017). In observational epidemiologic studies, higher soluble Lp-PLA2 enzymatic activity has been correlated with increased risk for coronary heart disease; small molecule inhibitors of Lp-PLA2 have been developed for the treatment of coronary heart disease (Salaheen_2017 citing Di Angelantonio_2012). This study identified participants who are naturally deficient in the Lp-PLA2 enzyme including two homozygotes and 106 heterozygotes. A dose-dependent response relationship between genotype and enzymatic activity was observed, however, carriers of c.663+1G>A did not have a reduced risk of myocardial infarction (Salaheen_2017). These report(s) do not provide unequivocal conclusions about association of the variant with Platelet-Activating Factor Acetylhydrolase Deficiency and an associated risk for myocardial infarction and/or stroke. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory and the OMIM database have submitted clinical-significance assessments for this variant to ClinVar after 2014. The clinical diagnostic laboratory classified the variant as a risk factor for coronary heart disease citing overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at