rs5743703
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001318789.2(TLR2):c.1736G>A(p.Arg579His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000498 in 1,613,292 control chromosomes in the GnomAD database, including 2 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 Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R579C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001318789.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR2 | NM_001318789.2 | c.1736G>A | p.Arg579His | missense_variant | 3/3 | ENST00000642700.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR2 | ENST00000642700.2 | c.1736G>A | p.Arg579His | missense_variant | 3/3 | NM_001318789.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00265 AC: 403AN: 151866Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000690 AC: 173AN: 250598Hom.: 0 AF XY: 0.000517 AC XY: 70AN XY: 135450
GnomAD4 exome AF: 0.000272 AC: 398AN: 1461308Hom.: 0 Cov.: 34 AF XY: 0.000257 AC XY: 187AN XY: 726968
GnomAD4 genome ? AF: 0.00266 AC: 405AN: 151984Hom.: 2 Cov.: 32 AF XY: 0.00252 AC XY: 187AN XY: 74276
ClinVar
Submissions by phenotype
TLR2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 15, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at