chr15-89665766-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002666.5(PLIN1):c.1386C>T(p.Pro462=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000358 in 1,274,134 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P462P) has been classified as Likely benign.
Frequency
Consequence
NM_002666.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN1 | NM_002666.5 | c.1386C>T | p.Pro462= | synonymous_variant | 9/9 | ENST00000300055.10 | |
PLIN1 | NM_001145311.2 | c.1386C>T | p.Pro462= | synonymous_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN1 | ENST00000300055.10 | c.1386C>T | p.Pro462= | synonymous_variant | 9/9 | 1 | NM_002666.5 | P1 | |
PLIN1 | ENST00000430628.2 | c.1386C>T | p.Pro462= | synonymous_variant | 9/9 | 5 | P1 | ||
PLIN1 | ENST00000560330.1 | c.124-825C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000186 AC: 28AN: 150778Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00263 AC: 6AN: 2284Hom.: 0 AF XY: 0.00326 AC XY: 5AN XY: 1534
GnomAD4 exome AF: 0.000381 AC: 428AN: 1123250Hom.: 1 Cov.: 31 AF XY: 0.000399 AC XY: 216AN XY: 540898
GnomAD4 genome AF: 0.000186 AC: 28AN: 150884Hom.: 0 Cov.: 32 AF XY: 0.000176 AC XY: 13AN XY: 73726
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at