rs5743845
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_017442.4(TLR9):c.2588G>A(p.Arg863Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00738 in 1,613,954 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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.
Frequency
Consequence
NM_017442.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR9 | NM_017442.4 | c.2588G>A | p.Arg863Gln | missense_variant | 2/2 | ENST00000360658.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR9 | ENST00000360658.3 | c.2588G>A | p.Arg863Gln | missense_variant | 2/2 | 1 | NM_017442.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0125 AC: 1903AN: 152204Hom.: 33 Cov.: 33
GnomAD3 exomes AF: 0.00826 AC: 2072AN: 250958Hom.: 30 AF XY: 0.00867 AC XY: 1178AN XY: 135822
GnomAD4 exome AF: 0.00685 AC: 10010AN: 1461632Hom.: 98 Cov.: 30 AF XY: 0.00732 AC XY: 5325AN XY: 727134
GnomAD4 genome AF: 0.0125 AC: 1902AN: 152322Hom.: 33 Cov.: 33 AF XY: 0.0122 AC XY: 907AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at