rs8179072
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_002666.5(PLIN1):c.1157C>T(p.Ala386Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000638 in 1,614,058 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 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000062 ( 0 hom. )
Consequence
PLIN1
NM_002666.5 missense
NM_002666.5 missense
Scores
2
6
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.67
Genes affected
PLIN1 (HGNC:9076): (perilipin 1) The protein encoded by this gene coats lipid storage droplets in adipocytes, thereby protecting them until they can be broken down by hormone-sensitive lipase. The encoded protein is the major cAMP-dependent protein kinase substrate in adipocytes and, when unphosphorylated, may play a role in the inhibition of lipolysis. Alternatively spliced transcript variants varying in the 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Feb 2009]
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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 (MetaRNN=0.031695217).
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000788 (12/152344) while in subpopulation EAS AF= 0.00174 (9/5178). AF 95% confidence interval is 0.000907. There are 0 homozygotes in gnomad4. There are 6 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLIN1 | NM_002666.5 | c.1157C>T | p.Ala386Val | missense_variant | 8/9 | ENST00000300055.10 | NP_002657.3 | |
PLIN1 | NM_001145311.2 | c.1157C>T | p.Ala386Val | missense_variant | 8/9 | NP_001138783.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.1157C>T | p.Ala386Val | missense_variant | 8/9 | 1 | NM_002666.5 | ENSP00000300055.5 | ||
PLIN1 | ENST00000430628.2 | c.1157C>T | p.Ala386Val | missense_variant | 8/9 | 5 | ENSP00000402167.2 | |||
PLIN1 | ENST00000560330.1 | c.123+110C>T | intron_variant | 5 | ENSP00000453426.1 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152226Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000163 AC: 41AN: 251012Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135698
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GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461714Hom.: 0 Cov.: 32 AF XY: 0.0000578 AC XY: 42AN XY: 727168
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GnomAD4 genome AF: 0.0000788 AC: 12AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74498
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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