rs1739654
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_004139.5(LBP):āc.144A>Gā(p.Leu48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 1,608,104 control chromosomes in the GnomAD database, including 710,426 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.90 ( 61637 hom., cov: 31)
Exomes š: 0.94 ( 648789 hom. )
Consequence
LBP
NM_004139.5 synonymous
NM_004139.5 synonymous
Scores
1
Clinical Significance
Conservation
PhyloP100: 0.787
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 20-38349567-A-G is Benign according to our data. Variant chr20-38349567-A-G is described in ClinVar as [Benign]. Clinvar id is 769090.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.787 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LBP | NM_004139.5 | c.144A>G | p.Leu48= | synonymous_variant | 2/15 | ENST00000217407.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LBP | ENST00000217407.3 | c.144A>G | p.Leu48= | synonymous_variant | 2/15 | 1 | NM_004139.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.898 AC: 136455AN: 152028Hom.: 61600 Cov.: 31
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GnomAD4 exome AF: 0.943 AC: 1373147AN: 1455958Hom.: 648789 Cov.: 50 AF XY: 0.941 AC XY: 681195AN XY: 723528
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GnomAD4 genome ? AF: 0.897 AC: 136545AN: 152146Hom.: 61637 Cov.: 31 AF XY: 0.896 AC XY: 66691AN XY: 74400
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at