rs73025939
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003265.3(TLR3):c.1927C>A(p.Arg643Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00182 in 1,605,718 control chromosomes in the GnomAD database, including 49 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 (★★).
Frequency
Consequence
NM_003265.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TLR3 | NM_003265.3 | c.1927C>A | p.Arg643Ser | missense_variant | 4/5 | ENST00000296795.8 | NP_003256.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLR3 | ENST00000296795.8 | c.1927C>A | p.Arg643Ser | missense_variant | 4/5 | 1 | NM_003265.3 | ENSP00000296795 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00955 AC: 1453AN: 152158Hom.: 30 Cov.: 33
GnomAD3 exomes AF: 0.00239 AC: 581AN: 243514Hom.: 7 AF XY: 0.00178 AC XY: 234AN XY: 131802
GnomAD4 exome AF: 0.00101 AC: 1465AN: 1453442Hom.: 19 Cov.: 36 AF XY: 0.000889 AC XY: 642AN XY: 722288
GnomAD4 genome AF: 0.00956 AC: 1456AN: 152276Hom.: 30 Cov.: 33 AF XY: 0.00911 AC XY: 678AN XY: 74450
ClinVar
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at