chr15-89665757-G-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002666.5(PLIN1):c.1395C>A(p.Pro465=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,273,980 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 2 hom. )
Consequence
PLIN1
NM_002666.5 synonymous
NM_002666.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.07
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 15-89665757-G-T is Benign according to our data. Variant chr15-89665757-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3044124.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.07 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000199 (30/150880) while in subpopulation SAS AF= 0.00518 (25/4826). AF 95% confidence interval is 0.0036. There are 1 homozygotes in gnomad4. There are 21 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 30 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN1 | NM_002666.5 | c.1395C>A | p.Pro465= | synonymous_variant | 9/9 | ENST00000300055.10 | |
PLIN1 | NM_001145311.2 | c.1395C>A | p.Pro465= | synonymous_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.1395C>A | p.Pro465= | synonymous_variant | 9/9 | 1 | NM_002666.5 | P1 | |
PLIN1 | ENST00000430628.2 | c.1395C>A | p.Pro465= | synonymous_variant | 9/9 | 5 | P1 | ||
PLIN1 | ENST00000560330.1 | c.124-816C>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000199 AC: 30AN: 150772Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00355 AC: 17AN: 4788Hom.: 0 AF XY: 0.00397 AC XY: 13AN XY: 3272
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GnomAD4 exome AF: 0.000239 AC: 268AN: 1123100Hom.: 2 Cov.: 31 AF XY: 0.000314 AC XY: 170AN XY: 540948
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PLIN1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 13, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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