8-19939200-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The ENST00000524029.5(LPL):c.-153-88G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 579,844 control chromosomes in the GnomAD database, including 3 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
ENST00000524029.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LPL | ENST00000524029.5 | c.-153-88G>C | intron_variant | Intron 1 of 3 | 4 | ENSP00000428237.1 | ||||
LPL | ENST00000520959.5 | c.-140-8980G>C | intron_variant | Intron 1 of 4 | 4 | ENSP00000428496.1 | ||||
LPL | ENST00000522701.5 | c.-218-23G>C | intron_variant | Intron 1 of 3 | 4 | ENSP00000428557.1 |
Frequencies
GnomAD3 genomes AF: 0.000992 AC: 151AN: 152182Hom.: 2 Cov.: 33
GnomAD4 exome AF: 0.00131 AC: 561AN: 427544Hom.: 1 Cov.: 0 AF XY: 0.00125 AC XY: 280AN XY: 224038
GnomAD4 genome AF: 0.000991 AC: 151AN: 152300Hom.: 2 Cov.: 33 AF XY: 0.000873 AC XY: 65AN XY: 74466
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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Identified in patients with familial combined hyperlipidemia and severe HDL deficiency in published literature (PMID: 9017514, 30333156); Located in the 5' untranslated region of the LPL gene and does not create a new start codon or alter the Kozak sequence; Published functional studies showed a reduction in promotor activity (PMID: 9017514); Also known as c.-53 G>C; This variant is associated with the following publications: (PMID: 34426522, 27055971, 9017514, 30333156) -
not specified Uncertain:1
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LPL-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at