rs3751542
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000236.3(LIPC):c.1388+111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 899,372 control chromosomes in the GnomAD database, including 47,326 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.35 ( 10215 hom., cov: 32)
Exomes 𝑓: 0.31 ( 37111 hom. )
Consequence
LIPC
NM_000236.3 intron
NM_000236.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.577
Genes affected
LIPC (HGNC:6619): (lipase C, hepatic type) Enables phospholipase A1 activity and triglyceride lipase activity. Involved in several processes, including lipid homeostasis; plasma lipoprotein particle remodeling; and triglyceride catabolic process. Located in extracellular space. Implicated in several diseases, including Alzheimer's disease; coronary artery disease; familial combined hyperlipidemia; peripheral vascular disease; and type 2 diabetes mellitus. Biomarker of hyperinsulinism; obesity; and type 1 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 15-58563834-T-C is Benign according to our data. Variant chr15-58563834-T-C is described in ClinVar as [Benign]. Clinvar id is 1264051.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-58563834-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPC | NM_000236.3 | c.1388+111T>C | intron_variant | ENST00000299022.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPC | ENST00000299022.10 | c.1388+111T>C | intron_variant | 1 | NM_000236.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.354 AC: 53852AN: 151920Hom.: 10212 Cov.: 32
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GnomAD4 exome AF: 0.306 AC: 228493AN: 747334Hom.: 37111 Cov.: 10 AF XY: 0.300 AC XY: 117743AN XY: 391948
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GnomAD4 genome ? AF: 0.355 AC: 53899AN: 152038Hom.: 10215 Cov.: 32 AF XY: 0.353 AC XY: 26242AN XY: 74314
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at