rs1554973
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138554.5(TLR4):c.*3886T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,840 control chromosomes in the GnomAD database, including 14,102 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 0.37 ( 14102 hom., cov: 31)
Exomes 𝑓: 0.33 ( 0 hom. )
Consequence
TLR4
NM_138554.5 3_prime_UTR
NM_138554.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.808
Genes affected
TLR4 (HGNC:11850): (toll like receptor 4) The protein encoded by this gene is a member of the Toll-like receptor (TLR) family which plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. They recognize pathogen-associated molecular patterns that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity. The various TLRs exhibit different patterns of expression. In silico studies have found a particularly strong binding of surface TLR4 with the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus disease-2019 (COVID-19). This receptor has also been implicated in signal transduction events induced by lipopolysaccharide (LPS) found in most gram-negative bacteria. Mutations in this gene have been associated with differences in LPS responsiveness, and with susceptibility to age-related macular degeneration. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2020]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR4 | NM_138554.5 | c.*3886T>C | 3_prime_UTR_variant | 3/3 | ENST00000355622.8 | ||
TLR4 | NM_003266.4 | c.*3886T>C | 3_prime_UTR_variant | 4/4 | |||
TLR4 | NM_138557.3 | c.*3886T>C | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR4 | ENST00000355622.8 | c.*3886T>C | 3_prime_UTR_variant | 3/3 | 1 | NM_138554.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.374 AC: 56715AN: 151716Hom.: 14062 Cov.: 31
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GnomAD4 exome AF: 0.333 AC: 2AN: 6Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1AN XY: 4
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GnomAD4 genome ? AF: 0.374 AC: 56819AN: 151834Hom.: 14102 Cov.: 31 AF XY: 0.369 AC XY: 27384AN XY: 74198
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at