rs1046587
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001143919.3(LTB4R):c.*144G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 624,980 control chromosomes in the GnomAD database, including 63,856 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 0.39 ( 12810 hom., cov: 33)
Exomes 𝑓: 0.45 ( 51046 hom. )
Consequence
LTB4R
NM_001143919.3 3_prime_UTR
NM_001143919.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.446
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTB4R | NM_001143919.3 | c.*144G>A | 3_prime_UTR_variant | 2/2 | ENST00000345363.8 | ||
LTB4R | NM_181657.3 | c.*144G>A | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTB4R | ENST00000345363.8 | c.*144G>A | 3_prime_UTR_variant | 2/2 | 1 | NM_001143919.3 | P1 | ||
LTB4R | ENST00000396782.2 | c.*144G>A | 3_prime_UTR_variant | 2/2 | 1 | P1 | |||
LTB4R | ENST00000396789.4 | c.*144G>A | 3_prime_UTR_variant | 2/2 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.389 AC: 59091AN: 152028Hom.: 12806 Cov.: 33
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GnomAD4 exome AF: 0.454 AC: 214606AN: 472834Hom.: 51046 Cov.: 7 AF XY: 0.451 AC XY: 109047AN XY: 241618
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GnomAD4 genome ? AF: 0.389 AC: 59113AN: 152146Hom.: 12810 Cov.: 33 AF XY: 0.383 AC XY: 28483AN XY: 74388
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at