rs759726625
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS2_Supporting
The NM_002666.5(PLIN1):c.991C>T(p.Leu331Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,461,356 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L331L) has been classified as Likely benign.
Frequency
Consequence
NM_002666.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN1 | NM_002666.5 | c.991C>T | p.Leu331Phe | missense_variant | 8/9 | ENST00000300055.10 | |
PLIN1 | NM_001145311.2 | c.991C>T | p.Leu331Phe | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.991C>T | p.Leu331Phe | missense_variant | 8/9 | 1 | NM_002666.5 | P1 | |
PLIN1 | ENST00000430628.2 | c.991C>T | p.Leu331Phe | missense_variant | 8/9 | 5 | P1 | ||
PLIN1 | ENST00000560330.1 | c.67C>T | p.Leu23Phe | missense_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250108Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135412
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461356Hom.: 0 Cov.: 36 AF XY: 0.0000110 AC XY: 8AN XY: 727002
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Monogenic diabetes Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | May 22, 2017 | ACMG Criteria:BP4 (9 predictors) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at