rs5743842
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_017442.4(TLR9):c.13C>T(p.Arg5Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00257 in 1,578,892 control chromosomes in the GnomAD database, including 88 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R5H) has been classified as Uncertain significance.
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.13C>T | p.Arg5Cys | missense_variant | 2/2 | ENST00000360658.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR9 | ENST00000360658.3 | c.13C>T | p.Arg5Cys | missense_variant | 2/2 | 1 | NM_017442.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0131 AC: 1994AN: 152104Hom.: 35 Cov.: 33
GnomAD3 exomes AF: 0.00360 AC: 677AN: 187814Hom.: 13 AF XY: 0.00266 AC XY: 268AN XY: 100734
GnomAD4 exome AF: 0.00145 AC: 2062AN: 1426670Hom.: 53 Cov.: 36 AF XY: 0.00129 AC XY: 915AN XY: 706964
GnomAD4 genome AF: 0.0131 AC: 1998AN: 152222Hom.: 35 Cov.: 33 AF XY: 0.0128 AC XY: 956AN XY: 74430
ClinVar
Submissions by phenotype
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