chr15-89665766-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002666.5(PLIN1):c.1386C>G(p.Pro462=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000089 in 1,123,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P462P) has been classified as Likely benign.
Frequency
Consequence
NM_002666.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN1 | NM_002666.5 | c.1386C>G | p.Pro462= | synonymous_variant | 9/9 | ENST00000300055.10 | |
PLIN1 | NM_001145311.2 | c.1386C>G | p.Pro462= | synonymous_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.1386C>G | p.Pro462= | synonymous_variant | 9/9 | 1 | NM_002666.5 | P1 | |
PLIN1 | ENST00000430628.2 | c.1386C>G | p.Pro462= | synonymous_variant | 9/9 | 5 | P1 | ||
PLIN1 | ENST00000560330.1 | c.124-825C>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 8.90e-7 AC: 1AN: 1123252Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 540900
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
PLIN1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 15, 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.