rs255
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000237.3(LPL):c.775+37T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,581,682 control chromosomes in the GnomAD database, including 20,369 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.18 ( 2545 hom., cov: 33)
Exomes 𝑓: 0.16 ( 17824 hom. )
Consequence
LPL
NM_000237.3 intron
NM_000237.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0960
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 8-19954390-T-C is Benign according to our data. Variant chr8-19954390-T-C is described in ClinVar as [Benign]. Clinvar id is 1182670.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-19954390-T-C is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPL | NM_000237.3 | c.775+37T>C | intron_variant | ENST00000650287.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPL | ENST00000650287.1 | c.775+37T>C | intron_variant | NM_000237.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.176 AC: 26799AN: 152036Hom.: 2533 Cov.: 33
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GnomAD3 exomes AF: 0.167 AC: 41243AN: 247204Hom.: 3574 AF XY: 0.168 AC XY: 22481AN XY: 133784
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GnomAD4 exome AF: 0.155 AC: 221787AN: 1429528Hom.: 17824 Cov.: 26 AF XY: 0.157 AC XY: 112071AN XY: 713296
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GnomAD4 genome ? AF: 0.176 AC: 26835AN: 152154Hom.: 2545 Cov.: 33 AF XY: 0.176 AC XY: 13104AN XY: 74396
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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 | Apr 01, 2019 | - - |
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