rs913930
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138554.5(TLR4):c.*7083G>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 0.729 in 152,116 control chromosomes in the GnomAD database, including 41,391 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 0.73 ( 41391 hom., cov: 33)
Failed GnomAD Quality Control
Consequence
TLR4
NM_138554.5 3_prime_UTR
NM_138554.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.623
Publications
33 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TLR4 | NM_138554.5 | c.*7083G>A | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000355622.8 | NP_612564.1 | ||
TLR4 | NM_003266.4 | c.*7083G>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_003257.1 | |||
TLR4 | NM_138557.3 | c.*7083G>A | 3_prime_UTR_variant | Exon 2 of 2 | NP_612567.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLR4 | ENST00000355622.8 | c.*7083G>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_138554.5 | ENSP00000363089.5 | |||
ENSG00000285082 | ENST00000697666.1 | c.140+13002G>A | intron_variant | Intron 3 of 4 | ENSP00000513391.1 |
Frequencies
GnomAD3 genomes AF: 0.728 AC: 110716AN: 151998Hom.: 41321 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
110716
AN:
151998
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome AF: 0.729 AC: 110847AN: 152116Hom.: 41391 Cov.: 33 AF XY: 0.730 AC XY: 54259AN XY: 74346 show subpopulations
GnomAD4 genome
AF:
AC:
110847
AN:
152116
Hom.:
Cov.:
33
AF XY:
AC XY:
54259
AN XY:
74346
show subpopulations
African (AFR)
AF:
AC:
36086
AN:
41550
American (AMR)
AF:
AC:
11117
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
2386
AN:
3472
East Asian (EAS)
AF:
AC:
5122
AN:
5188
South Asian (SAS)
AF:
AC:
3720
AN:
4818
European-Finnish (FIN)
AF:
AC:
6259
AN:
10538
Middle Eastern (MID)
AF:
AC:
174
AN:
292
European-Non Finnish (NFE)
AF:
AC:
43924
AN:
67966
Other (OTH)
AF:
AC:
1497
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1471
2942
4413
5884
7355
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
828
1656
2484
3312
4140
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3071
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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