19-40366755-ACCT-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_012268.4(PLD3):c.103-9_103-7del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,248 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PLD3
NM_012268.4 splice_polypyrimidine_tract, intron
NM_012268.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0530
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 19-40366755-ACCT-A is Benign according to our data. Variant chr19-40366755-ACCT-A is described in ClinVar as [Likely_benign]. Clinvar id is 1917763.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLD3 | NM_012268.4 | c.103-9_103-7del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000409735.9 | NP_036400.2 | |||
PLD3 | NM_001031696.4 | c.103-9_103-7del | splice_polypyrimidine_tract_variant, intron_variant | NP_001026866.1 | ||||
PLD3 | NM_001291311.2 | c.103-9_103-7del | splice_polypyrimidine_tract_variant, intron_variant | NP_001278240.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLD3 | ENST00000409735.9 | c.103-9_103-7del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_012268.4 | ENSP00000386938 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151706Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461542Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 727076
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151706Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74050
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 25, 2022 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at