rs301
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000237.3(LPL):c.1139+43T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,607,608 control chromosomes in the GnomAD database, including 45,495 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.25 ( 4970 hom., cov: 31)
Exomes 𝑓: 0.24 ( 40525 hom. )
Consequence
LPL
NM_000237.3 intron
NM_000237.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.14
Genes affected
LPL (HGNC:6677): (lipoprotein lipase) LPL encodes lipoprotein lipase, which is expressed in heart, muscle, and adipose tissue. LPL functions as a homodimer, and has the dual functions of triglyceride hydrolase and ligand/bridging factor for receptor-mediated lipoprotein uptake. Severe mutations that cause LPL deficiency result in type I hyperlipoproteinemia, while less extreme mutations in LPL are linked to many disorders of lipoprotein metabolism. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
Variant 8-19959423-T-C is Benign according to our data. Variant chr8-19959423-T-C is described in ClinVar as [Benign]. Clinvar id is 1278475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-19959423-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LPL | NM_000237.3 | c.1139+43T>C | intron_variant | ENST00000650287.1 | NP_000228.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LPL | ENST00000650287.1 | c.1139+43T>C | intron_variant | NM_000237.3 | ENSP00000497642 | P1 | ||||
LPL | ENST00000650478.1 | c.80-1478T>C | intron_variant, NMD_transcript_variant | ENSP00000497560 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38561AN: 151894Hom.: 4962 Cov.: 31
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GnomAD3 exomes AF: 0.242 AC: 58705AN: 242970Hom.: 7026 AF XY: 0.240 AC XY: 31594AN XY: 131896
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GnomAD4 exome AF: 0.235 AC: 342332AN: 1455596Hom.: 40525 Cov.: 32 AF XY: 0.235 AC XY: 170364AN XY: 723906
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GnomAD4 genome AF: 0.254 AC: 38583AN: 152012Hom.: 4970 Cov.: 31 AF XY: 0.252 AC XY: 18700AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at