15-89665596-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4BS1_SupportingBS2
The NM_002666.5(PLIN1):āc.1556G>Cā(p.Arg519Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0002 in 1,527,004 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 Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R519L) has been classified 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN1 | NM_002666.5 | c.1556G>C | p.Arg519Pro | missense_variant | 9/9 | ENST00000300055.10 | |
PLIN1 | NM_001145311.2 | c.1556G>C | p.Arg519Pro | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.1556G>C | p.Arg519Pro | missense_variant | 9/9 | 1 | NM_002666.5 | P1 | |
PLIN1 | ENST00000430628.2 | c.1556G>C | p.Arg519Pro | missense_variant | 9/9 | 5 | P1 | ||
PLIN1 | ENST00000560330.1 | c.124-655G>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 151556Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000140 AC: 18AN: 128316Hom.: 0 AF XY: 0.000113 AC XY: 8AN XY: 70510
GnomAD4 exome AF: 0.000208 AC: 286AN: 1375448Hom.: 0 Cov.: 31 AF XY: 0.000209 AC XY: 142AN XY: 678822
GnomAD4 genome AF: 0.000132 AC: 20AN: 151556Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 73994
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 07, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at