14-24316578-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001143919.3(LTB4R):c.927C>T(p.Gly309Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,442,756 control chromosomes in the GnomAD database, including 18,843 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 0.13 ( 1911 hom., cov: 33)
Exomes 𝑓: 0.14 ( 16932 hom. )
Consequence
LTB4R
NM_001143919.3 synonymous
NM_001143919.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.383
Genes affected
LTB4R (HGNC:6713): (leukotriene B4 receptor) Predicted to enable G protein-coupled peptide receptor activity and leukotriene B4 receptor activity. Predicted to be involved in inflammatory response and neuropeptide signaling pathway. Predicted to act upstream of or within signal transduction. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
Synonymous conserved (PhyloP=-0.383 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTB4R | ENST00000345363.8 | c.927C>T | p.Gly309Gly | synonymous_variant | Exon 2 of 2 | 1 | NM_001143919.3 | ENSP00000307445.3 | ||
LTB4R | ENST00000396782.2 | c.927C>T | p.Gly309Gly | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000380002.2 | |||
LTB4R | ENST00000396789.4 | c.927C>T | p.Gly309Gly | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000380008.4 | |||
LTB4R | ENST00000556141.1 | c.627C>T | p.Gly209Gly | synonymous_variant | Exon 2 of 2 | 3 | ENSP00000451929.1 |
Frequencies
GnomAD3 genomes AF: 0.134 AC: 20325AN: 151934Hom.: 1916 Cov.: 33
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GnomAD3 exomes AF: 0.226 AC: 10719AN: 47400Hom.: 1596 AF XY: 0.225 AC XY: 6299AN XY: 27956
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GnomAD4 exome AF: 0.137 AC: 177265AN: 1290714Hom.: 16932 Cov.: 32 AF XY: 0.141 AC XY: 89116AN XY: 633110
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GnomAD4 genome AF: 0.134 AC: 20306AN: 152042Hom.: 1911 Cov.: 33 AF XY: 0.143 AC XY: 10616AN XY: 74322
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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