rs17363814
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005817.5(PLIN3):c.960+47G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000258 in 1,553,246 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000067 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PLIN3
NM_005817.5 intron
NM_005817.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.444
Genes affected
PLIN3 (HGNC:16893): (perilipin 3) Mannose 6-phophate receptors (MPRs) deliver lysosomal hydrolase from the Golgi to endosomes and then return to the Golgi complex. The protein encoded by this gene interacts with the cytoplasmic domains of both cation-independent and cation-dependent MPRs, and is required for endosome-to-Golgi transport. This protein also binds directly to the GTPase RAB9 (RAB9A), a member of the RAS oncogene family. The interaction with RAB9 has been shown to increase the affinity of this protein for its cargo. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN3 | NM_005817.5 | c.960+47G>T | intron_variant | ENST00000221957.9 | |||
PLIN3 | NM_001164189.2 | c.960+47G>T | intron_variant | ||||
PLIN3 | NM_001164194.2 | c.924+47G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN3 | ENST00000221957.9 | c.960+47G>T | intron_variant | 1 | NM_005817.5 | P3 | |||
PLIN3 | ENST00000585479.5 | c.960+47G>T | intron_variant | 1 | A1 | ||||
PLIN3 | ENST00000589163.5 | c.533+47G>T | intron_variant | 3 | |||||
PLIN3 | ENST00000592528.5 | c.924+47G>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000670 AC: 1AN: 149188Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000563 AC: 1AN: 177610Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 95748
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GnomAD4 exome AF: 0.00000214 AC: 3AN: 1404058Hom.: 0 Cov.: 28 AF XY: 0.00000288 AC XY: 2AN XY: 694878
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GnomAD4 genome ? AF: 0.00000670 AC: 1AN: 149188Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72656
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ClinVar
Not reported inComputational scores
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at