rs139854420
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003265.3(TLR3):c.165G>A(p.Val55=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,614,134 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V55V) has been classified as Likely benign.
Frequency
Consequence
NM_003265.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR3 | NM_003265.3 | c.165G>A | p.Val55= | synonymous_variant | 2/5 | ENST00000296795.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR3 | ENST00000296795.8 | c.165G>A | p.Val55= | synonymous_variant | 2/5 | 1 | NM_003265.3 | P1 | |
TLR3 | ENST00000513189.1 | c.165G>A | p.Val55= | synonymous_variant | 2/5 | 1 | |||
TLR3 | ENST00000698351.1 | c.165G>A | p.Val55= | synonymous_variant | 2/5 | ||||
TLR3 | ENST00000698352.1 | c.165G>A | p.Val55= | synonymous_variant, NMD_transcript_variant | 2/5 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251458Hom.: 1 AF XY: 0.0000662 AC XY: 9AN XY: 135904
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461894Hom.: 2 Cov.: 32 AF XY: 0.0000564 AC XY: 41AN XY: 727248
GnomAD4 genome AF: 0.000263 AC: 40AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74432
ClinVar
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at