rs17363814
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -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
Publications
14 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -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 rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PLIN3 | NM_005817.5 | c.960+47G>T | intron_variant | Intron 7 of 7 | ENST00000221957.9 | NP_005808.3 | ||
| PLIN3 | NM_001164189.2 | c.960+47G>T | intron_variant | Intron 7 of 7 | NP_001157661.1 | |||
| PLIN3 | NM_001164194.2 | c.924+47G>T | intron_variant | Intron 7 of 7 | NP_001157666.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PLIN3 | ENST00000221957.9 | c.960+47G>T | intron_variant | Intron 7 of 7 | 1 | NM_005817.5 | ENSP00000221957.3 | |||
| PLIN3 | ENST00000585479.5 | c.960+47G>T | intron_variant | Intron 7 of 7 | 1 | ENSP00000465596.1 | ||||
| PLIN3 | ENST00000592528.5 | c.924+47G>T | intron_variant | Intron 7 of 7 | 2 | ENSP00000467803.1 | ||||
| PLIN3 | ENST00000589163.5 | c.531+47G>T | intron_variant | Intron 4 of 4 | 3 | ENSP00000468476.1 |
Frequencies
GnomAD3 genomes 0.00000670 AC: 1AN: 149188Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
149188
Hom.:
Cov.:
31
Gnomad AFR
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000563 AC: 1AN: 177610 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
177610
AF XY:
Gnomad AFR exome
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Gnomad ASJ exome
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GnomAD4 exome AF: 0.00000214 AC: 3AN: 1404058Hom.: 0 Cov.: 28 AF XY: 0.00000288 AC XY: 2AN XY: 694878 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1404058
Hom.:
Cov.:
28
AF XY:
AC XY:
2
AN XY:
694878
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31556
American (AMR)
AF:
AC:
0
AN:
35070
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22898
East Asian (EAS)
AF:
AC:
0
AN:
38622
South Asian (SAS)
AF:
AC:
0
AN:
78356
European-Finnish (FIN)
AF:
AC:
0
AN:
50750
Middle Eastern (MID)
AF:
AC:
0
AN:
4092
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1084944
Other (OTH)
AF:
AC:
0
AN:
57770
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
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1
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Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.00000670 AC: 1AN: 149188Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72656 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
149188
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
72656
show subpopulations
African (AFR)
AF:
AC:
0
AN:
40158
American (AMR)
AF:
AC:
0
AN:
14840
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3458
East Asian (EAS)
AF:
AC:
0
AN:
5148
South Asian (SAS)
AF:
AC:
0
AN:
4618
European-Finnish (FIN)
AF:
AC:
0
AN:
10414
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67316
Other (OTH)
AF:
AC:
0
AN:
2026
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.775
Heterozygous variant carriers
0
0
1
1
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2
0.00
0.20
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0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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