9-117712405-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_138554.5(TLR4):c.277A>G(p.Ile93Val) variant causes a missense change. The variant allele was found at a frequency of 0.000164 in 1,613,864 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 4 hom. )
Consequence
TLR4
NM_138554.5 missense
NM_138554.5 missense
Scores
2
5
10
Clinical Significance
Conservation
PhyloP100: 5.53
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.020430148).
BP6
?
Variant 9-117712405-A-G is Benign according to our data. Variant chr9-117712405-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3048219.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR4 | NM_138554.5 | c.277A>G | p.Ile93Val | missense_variant | 3/3 | ENST00000355622.8 | |
TLR4 | NM_003266.4 | c.157A>G | p.Ile53Val | missense_variant | 4/4 | ||
TLR4 | NM_138557.3 | c.-324A>G | 5_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR4 | ENST00000355622.8 | c.277A>G | p.Ile93Val | missense_variant | 3/3 | 1 | NM_138554.5 | P1 | |
TLR4 | ENST00000394487.5 | c.157A>G | p.Ile53Val | missense_variant | 4/4 | 1 | |||
TLR4 | ENST00000472304.2 | c.*11A>G | 3_prime_UTR_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152188Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
17
AN:
152188
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.000387 AC: 97AN: 250620Hom.: 1 AF XY: 0.000487 AC XY: 66AN XY: 135452
GnomAD3 exomes
AF:
AC:
97
AN:
250620
Hom.:
AF XY:
AC XY:
66
AN XY:
135452
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000169 AC: 247AN: 1461558Hom.: 4 Cov.: 31 AF XY: 0.000232 AC XY: 169AN XY: 727072
GnomAD4 exome
AF:
AC:
247
AN:
1461558
Hom.:
Cov.:
31
AF XY:
AC XY:
169
AN XY:
727072
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74458
GnomAD4 genome
?
AF:
AC:
17
AN:
152306
Hom.:
Cov.:
32
AF XY:
AC XY:
11
AN XY:
74458
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
?
AF:
AC:
60
Asia WGS
AF:
AC:
1
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TLR4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 16, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;.;N
REVEL
Benign
Sift
Pathogenic
D;.;D
Sift4G
Uncertain
D;.;D
Polyphen
1.0
.;D;D
Vest4
MutPred
0.33
.;Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);
MVP
MPC
0.10
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at