15-89665872-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002666.5(PLIN1):c.1280A>G(p.Glu427Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000397 in 1,510,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.1280A>G | p.Glu427Gly | missense_variant | 9/9 | ENST00000300055.10 | |
PLIN1 | NM_001145311.2 | c.1280A>G | p.Glu427Gly | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.1280A>G | p.Glu427Gly | missense_variant | 9/9 | 1 | NM_002666.5 | P1 | |
PLIN1 | ENST00000430628.2 | c.1280A>G | p.Glu427Gly | missense_variant | 9/9 | 5 | P1 | ||
PLIN1 | ENST00000560330.1 | c.124-931A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151988Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000368 AC: 5AN: 1358064Hom.: 0 Cov.: 31 AF XY: 0.00000149 AC XY: 1AN XY: 670932
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151988Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74234
ClinVar
Submissions by phenotype
PLIN1-related familial partial lipodystrophy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 15, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at