rs111663599
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002666.5(PLIN1):c.466G>T(p.Val156Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,614,048 control chromosomes in the GnomAD database, including 199 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002666.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN1 | NM_002666.5 | c.466G>T | p.Val156Leu | missense_variant | 5/9 | ENST00000300055.10 | |
PLIN1 | NM_001145311.2 | c.466G>T | p.Val156Leu | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.466G>T | p.Val156Leu | missense_variant | 5/9 | 1 | NM_002666.5 | P1 | |
PLIN1 | ENST00000430628.2 | c.466G>T | p.Val156Leu | missense_variant | 5/9 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0104 AC: 1585AN: 152222Hom.: 23 Cov.: 32
GnomAD3 exomes AF: 0.0125 AC: 3136AN: 250760Hom.: 51 AF XY: 0.0125 AC XY: 1701AN XY: 135592
GnomAD4 exome AF: 0.0110 AC: 16084AN: 1461708Hom.: 176 Cov.: 35 AF XY: 0.0107 AC XY: 7764AN XY: 727142
GnomAD4 genome AF: 0.0104 AC: 1583AN: 152340Hom.: 23 Cov.: 32 AF XY: 0.0121 AC XY: 902AN XY: 74486
ClinVar
Submissions by phenotype
Monogenic diabetes Benign:1
Benign, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | Feb 01, 2019 | ACMG criteria: BP4 (REVEL 0.046 + 8 predictors), not using PP3 (2 predictors)), BA1 (5.3% in gnomAD EF, MAF 1.5% overall), BS2 (204 cases and 197 controls in type2diabetesgenetics.org)= benign - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | PLIN1: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at