rs2224122
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000396789.4(LTB4R):c.-828G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,276 control chromosomes in the GnomAD database, including 2,453 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 0.15 ( 2450 hom., cov: 32)
Exomes 𝑓: 0.29 ( 3 hom. )
Consequence
LTB4R
ENST00000396789.4 5_prime_UTR
ENST00000396789.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.65
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LTB4R | NM_001143919.3 | c.-15-1429G>C | intron_variant | ENST00000345363.8 | |||
LTB4R | NM_181657.3 | c.-828G>C | 5_prime_UTR_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTB4R | ENST00000396789.4 | c.-828G>C | 5_prime_UTR_variant | 1/2 | 1 | P1 | |||
LTB4R | ENST00000345363.8 | c.-15-1429G>C | intron_variant | 1 | NM_001143919.3 | P1 | |||
LTB4R | ENST00000553481.1 | c.-15-1429G>C | intron_variant | 2 | |||||
LTB4R | ENST00000556141.1 | c.-60+253G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.153 AC: 23314AN: 152122Hom.: 2449 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.289 AC: 11AN: 38Hom.: 3 Cov.: 0 AF XY: 0.318 AC XY: 7AN XY: 22
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GnomAD4 genome ? AF: 0.153 AC: 23318AN: 152238Hom.: 2450 Cov.: 32 AF XY: 0.149 AC XY: 11097AN XY: 74442
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at