rs2232592
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004139.5(LBP):c.588+40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00926 in 1,577,466 control chromosomes in the GnomAD database, including 604 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.020 ( 103 hom., cov: 31)
Exomes 𝑓: 0.0081 ( 501 hom. )
Consequence
LBP
NM_004139.5 intron
NM_004139.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.208
Genes affected
LBP (HGNC:6517): (lipopolysaccharide binding protein) The protein encoded by this gene is involved in the acute-phase immunologic response to gram-negative bacterial infections. Gram-negative bacteria contain a glycolipid, lipopolysaccharide (LPS), on their outer cell wall. Together with bactericidal permeability-increasing protein (BPI), the encoded protein binds LPS and interacts with the CD14 receptor, probably playing a role in regulating LPS-dependent monocyte responses. Studies in mice suggest that the encoded protein is necessary for the rapid acute-phase response to LPS but not for the clearance of LPS from circulation. This protein is part of a family of structurally and functionally related proteins, including BPI, plasma cholesteryl ester transfer protein (CETP), and phospholipid transfer protein (PLTP). [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LBP | NM_004139.5 | c.588+40G>A | intron_variant | ENST00000217407.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LBP | ENST00000217407.3 | c.588+40G>A | intron_variant | 1 | NM_004139.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0198 AC: 3017AN: 152176Hom.: 98 Cov.: 31
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GnomAD3 exomes AF: 0.0255 AC: 6342AN: 248636Hom.: 321 AF XY: 0.0214 AC XY: 2887AN XY: 134904
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GnomAD4 exome AF: 0.00811 AC: 11565AN: 1425172Hom.: 501 Cov.: 26 AF XY: 0.00756 AC XY: 5376AN XY: 711086
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GnomAD4 genome ? AF: 0.0200 AC: 3046AN: 152294Hom.: 103 Cov.: 31 AF XY: 0.0215 AC XY: 1601AN XY: 74460
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ClinVar
Not reported inComputational scores
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Name
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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