rs4986791
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138554.5(TLR4):c.1196C>T(p.Thr399Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 1,613,894 control chromosomes in the GnomAD database, including 3,597 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_138554.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR4 | NM_138554.5 | c.1196C>T | p.Thr399Ile | missense_variant | 3/3 | ENST00000355622.8 | |
TLR4 | NM_003266.4 | c.1076C>T | p.Thr359Ile | missense_variant | 4/4 | ||
TLR4 | NM_138557.3 | c.596C>T | p.Thr199Ile | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR4 | ENST00000355622.8 | c.1196C>T | p.Thr399Ile | missense_variant | 3/3 | 1 | NM_138554.5 | P1 | |
TLR4 | ENST00000394487.5 | c.1076C>T | p.Thr359Ile | missense_variant | 4/4 | 1 | |||
TLR4 | ENST00000472304.2 | c.*930C>T | 3_prime_UTR_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0494 AC: 7511AN: 152076Hom.: 250 Cov.: 32
GnomAD3 exomes AF: 0.0566 AC: 14176AN: 250350Hom.: 537 AF XY: 0.0602 AC XY: 8143AN XY: 135366
GnomAD4 exome AF: 0.0625 AC: 91406AN: 1461700Hom.: 3347 Cov.: 32 AF XY: 0.0636 AC XY: 46272AN XY: 727150
GnomAD4 genome AF: 0.0493 AC: 7509AN: 152194Hom.: 250 Cov.: 32 AF XY: 0.0525 AC XY: 3908AN XY: 74418
ClinVar
Submissions by phenotype
COPD, severe early onset Uncertain:1
Uncertain significance, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Sep 01, 2023 | - - |
TLR4 POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Jul 18, 2002 | - - |
not provided Other:1
not provided, no classification provided | literature only | NEI Ophthalmic Genomics Laboratory, National Institutes of Health | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at