chr1-223110872-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003268.6(TLR5):c.2160T>A(p.Ser720Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00305 in 1,614,248 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003268.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR5 | NM_003268.6 | c.2160T>A | p.Ser720Arg | missense_variant | 6/6 | ENST00000642603.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR5 | ENST00000642603.2 | c.2160T>A | p.Ser720Arg | missense_variant | 6/6 | NM_003268.6 | P1 | ||
TLR5 | ENST00000540964.5 | c.2160T>A | p.Ser720Arg | missense_variant | 4/4 | 5 | P1 | ||
TLR5 | ENST00000645434.1 | c.2160T>A | p.Ser720Arg | missense_variant | 5/5 |
Frequencies
GnomAD3 genomes ? AF: 0.00160 AC: 244AN: 152250Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00139 AC: 350AN: 251286Hom.: 2 AF XY: 0.00154 AC XY: 209AN XY: 135802
GnomAD4 exome AF: 0.00320 AC: 4680AN: 1461880Hom.: 14 Cov.: 33 AF XY: 0.00310 AC XY: 2256AN XY: 727236
GnomAD4 genome ? AF: 0.00160 AC: 244AN: 152368Hom.: 1 Cov.: 32 AF XY: 0.00136 AC XY: 101AN XY: 74514
ClinVar
Submissions by phenotype
TLR5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 10, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at