rs3829462
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000236.3(LIPC):c.1068C>A(p.Phe356Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 1,222,610 control chromosomes in the GnomAD database, including 576,991 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000236.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPC | NM_000236.3 | c.1068C>A | p.Phe356Leu | missense_variant | 7/9 | ENST00000299022.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPC | ENST00000299022.10 | c.1068C>A | p.Phe356Leu | missense_variant | 7/9 | 1 | NM_000236.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.946 AC: 143983AN: 152158Hom.: 68356 Cov.: 32
GnomAD3 exomes AF: 0.972 AC: 244028AN: 251044Hom.: 118756 AF XY: 0.975 AC XY: 132316AN XY: 135712
GnomAD4 exome AF: 0.974 AC: 1042863AN: 1070334Hom.: 508601 Cov.: 15 AF XY: 0.976 AC XY: 537307AN XY: 550598
GnomAD4 genome ? AF: 0.946 AC: 144068AN: 152276Hom.: 68390 Cov.: 32 AF XY: 0.946 AC XY: 70435AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2018 | This variant is associated with the following publications: (PMID: 27884173, 8732782, 20981092, 19428034) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Hyperlipidemia due to hepatic triglyceride lipase deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at