rs146385147
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_002666.5(PLIN1):c.1139C>T(p.Ala380Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,613,996 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002666.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.1139C>T | p.Ala380Val | missense_variant | Exon 8 of 9 | 1 | NM_002666.5 | ENSP00000300055.5 | ||
PLIN1 | ENST00000430628.2 | c.1139C>T | p.Ala380Val | missense_variant | Exon 8 of 9 | 5 | ENSP00000402167.2 | |||
PLIN1 | ENST00000560330.1 | c.123+92C>T | intron_variant | Intron 2 of 2 | 5 | ENSP00000453426.1 |
Frequencies
GnomAD3 genomes AF: 0.00571 AC: 869AN: 152210Hom.: 10 Cov.: 33
GnomAD3 exomes AF: 0.00144 AC: 361AN: 251128Hom.: 1 AF XY: 0.000943 AC XY: 128AN XY: 135772
GnomAD4 exome AF: 0.000581 AC: 849AN: 1461666Hom.: 7 Cov.: 32 AF XY: 0.000488 AC XY: 355AN XY: 727138
GnomAD4 genome AF: 0.00572 AC: 871AN: 152330Hom.: 10 Cov.: 33 AF XY: 0.00571 AC XY: 425AN XY: 74488
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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Monogenic diabetes Benign:1
ACMG criteria: BA1 (2.1% MAF in gnomAD Africans), BS2 (66 cases and 47 controls in T2DM)= benign (REVEL 0.199 + PP3/3 predictors + BP4/7 predictors: conflicting evidence, not using) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at