rs78098893
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003268.6(TLR5):āc.2254A>Gā(p.Arg752Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000481 in 1,614,264 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0027 ( 3 hom., cov: 32)
Exomes š: 0.00025 ( 0 hom. )
Consequence
TLR5
NM_003268.6 missense
NM_003268.6 missense
Scores
1
8
7
Clinical Significance
Conservation
PhyloP100: 1.15
Genes affected
TLR5 (HGNC:11851): (toll like receptor 5) This gene encodes a member of the toll-like receptor (TLR) family, which plays a fundamental role in pathogen recognition and activation of innate immune responses. These receptors recognize distinct pathogen-associated molecular patterns that are expressed on infectious agents. The protein encoded by this gene recognizes bacterial flagellin, the principal component of bacterial flagella and a virulence factor. The activation of this receptor mobilizes the nuclear factor NF-kappaB, which in turn activates a host of inflammatory-related target genes. Mutations in this gene have been associated with both resistance and susceptibility to systemic lupus erythematosus, and susceptibility to Legionnaire disease.[provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0147899985).
BP6
?
Variant 1-223110778-T-C is Benign according to our data. Variant chr1-223110778-T-C is described in ClinVar as [Benign]. Clinvar id is 791835.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR5 | NM_003268.6 | c.2254A>G | p.Arg752Gly | missense_variant | 6/6 | ENST00000642603.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR5 | ENST00000642603.2 | c.2254A>G | p.Arg752Gly | missense_variant | 6/6 | NM_003268.6 | P1 | ||
TLR5 | ENST00000540964.5 | c.2254A>G | p.Arg752Gly | missense_variant | 4/4 | 5 | P1 | ||
TLR5 | ENST00000645434.1 | c.2254A>G | p.Arg752Gly | missense_variant | 5/5 |
Frequencies
GnomAD3 genomes ? AF: 0.00269 AC: 409AN: 152262Hom.: 3 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000712 AC: 179AN: 251366Hom.: 0 AF XY: 0.000537 AC XY: 73AN XY: 135846
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GnomAD4 exome AF: 0.000252 AC: 368AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.000198 AC XY: 144AN XY: 727242
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GnomAD4 genome ? AF: 0.00268 AC: 409AN: 152380Hom.: 3 Cov.: 32 AF XY: 0.00255 AC XY: 190AN XY: 74520
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;.;.;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;D;.
REVEL
Benign
Sift
Uncertain
D;.;D;.
Sift4G
Uncertain
D;.;D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
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