chr9-117712651-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.523A>G(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 (★). 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
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ACMG classification
Verdict is Likely_benign. Variant got -6 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