rs4490097
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012268.4(PLD3):c.-279+7049A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,784 control chromosomes in the GnomAD database, including 12,131 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 0.37 ( 12126 hom., cov: 29)
Exomes 𝑓: 0.58 ( 5 hom. )
Consequence
PLD3
NM_012268.4 intron
NM_012268.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.368
Genes affected
PLD3 (HGNC:17158): (phospholipase D family member 3) This gene encodes a member of the phospholipase D (PLD) family of enzymes that catalyze the hydrolysis of membrane phospholipids. The encoded protein is a single-pass type II membrane protein and contains two PLD phosphodiesterase domains. This protein influences processing of amyloid-beta precursor protein. Mutations in this gene are associated with Alzheimer disease risk. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLD3 | NM_012268.4 | c.-279+7049A>C | intron_variant | ENST00000409735.9 | |||
PLD3 | NM_001031696.4 | c.-99+7093A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLD3 | ENST00000409735.9 | c.-279+7049A>C | intron_variant | 1 | NM_012268.4 | P1 | |||
ENST00000622968.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.374 AC: 56655AN: 151640Hom.: 12129 Cov.: 29
GnomAD3 genomes
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GnomAD4 exome AF: 0.577 AC: 15AN: 26Hom.: 5 Cov.: 0 AF XY: 0.545 AC XY: 12AN XY: 22
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GnomAD4 genome ? AF: 0.373 AC: 56661AN: 151758Hom.: 12126 Cov.: 29 AF XY: 0.375 AC XY: 27805AN XY: 74114
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at