chr9-117713029-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138554.5(TLR4):c.901A>G(p.Ile301Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_138554.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR4 | NM_138554.5 | c.901A>G | p.Ile301Val | missense_variant | 3/3 | ENST00000355622.8 | |
TLR4 | NM_003266.4 | c.781A>G | p.Ile261Val | missense_variant | 4/4 | ||
TLR4 | NM_138557.3 | c.301A>G | p.Ile101Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR4 | ENST00000355622.8 | c.901A>G | p.Ile301Val | missense_variant | 3/3 | 1 | NM_138554.5 | P1 | |
TLR4 | ENST00000394487.5 | c.781A>G | p.Ile261Val | missense_variant | 4/4 | 1 | |||
TLR4 | ENST00000472304.2 | c.*635A>G | 3_prime_UTR_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250864Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135564
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461758Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727184
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.901A>G (p.I301V) alteration is located in exon 3 (coding exon 3) of the TLR4 gene. This alteration results from a A to G substitution at nucleotide position 901, causing the isoleucine (I) at amino acid position 301 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at