rs5743708
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001318789.2(TLR2):c.2258G>A(p.Arg753Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0178 in 152062 control chromosomes in the gnomAD Genomes database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.018 ( 40 hom., cov: 32)
Exomes 𝑓: 0.017 ( 80 hom. )
Consequence
TLR2
NM_001318789.2 missense
NM_001318789.2 missense
Scores
4
2
7
Clinical Significance
Conservation
PhyloP100: 6.79
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009150982).
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.0178 (2701/152062) while in subpopulation NFE AF= 0.0294 (1999/67996). AF 95% confidence interval is 0.0283. There are 40 homozygotes in gnomad. There are 1269 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
?
High Homozygotes in GnomAd at 40 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR2 | NM_001318789.2 | c.2258G>A | p.Arg753Gln | missense_variant | 3/3 | ENST00000642700.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR2 | ENST00000642700.2 | c.2258G>A | p.Arg753Gln | missense_variant | 3/3 | NM_001318789.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0178 AC: 2701AN: 152062Hom.: 40 Cov.: 32
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32
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GnomAD3 exomes AF: 0.0174 AC: 4375AN: 251060Hom.: 80 AF XY: 0.0173 AC XY: 2355AN XY: 135790
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GnomAD4 exome AF: 0.0257 AC: 37626AN: 1461872Hom.: 592 AF XY: 0.0250 AC XY: 18208AN XY: 727234
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TwinsUK
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133
ALSPAC
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116
ESP6500AA
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23
ESP6500EA
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266
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2093
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3478
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ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Mycobacterium tuberculosis, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Nov 02, 2012 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;T;T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M;.
MutationTaster
Benign
D
PrimateAI
Uncertain
T
Polyphen
D;D;D;D;.
Vest4
0.20
MPC
0.43
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at