rs16906079
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_138554.5(TLR4):āc.523A>Gā(p.Thr175Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000514 in 1,613,610 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_138554.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR4 | NM_138554.5 | c.523A>G | p.Thr175Ala | missense_variant | 3/3 | ENST00000355622.8 | |
TLR4 | NM_003266.4 | c.403A>G | p.Thr135Ala | missense_variant | 4/4 | ||
TLR4 | NM_138557.3 | c.-78A>G | 5_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR4 | ENST00000355622.8 | c.523A>G | p.Thr175Ala | missense_variant | 3/3 | 1 | NM_138554.5 | P1 | |
TLR4 | ENST00000394487.5 | c.403A>G | p.Thr135Ala | missense_variant | 4/4 | 1 | |||
TLR4 | ENST00000472304.2 | c.*257A>G | 3_prime_UTR_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000493 AC: 75AN: 152130Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000651 AC: 163AN: 250362Hom.: 0 AF XY: 0.000665 AC XY: 90AN XY: 135342
GnomAD4 exome AF: 0.000517 AC: 755AN: 1461362Hom.: 6 Cov.: 32 AF XY: 0.000515 AC XY: 374AN XY: 726872
GnomAD4 genome ? AF: 0.000493 AC: 75AN: 152248Hom.: 1 Cov.: 32 AF XY: 0.000551 AC XY: 41AN XY: 74434
ClinVar
Submissions by phenotype
TLR4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 08, 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at