chr4-186076658-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_003265.3(TLR3):c.39C>T(p.Gly13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,096 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G13G) 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 -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLR3 | NM_003265.3 | c.39C>T | p.Gly13= | synonymous_variant | 2/5 | ENST00000296795.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLR3 | ENST00000296795.8 | c.39C>T | p.Gly13= | synonymous_variant | 2/5 | 1 | NM_003265.3 | P1 | |
TLR3 | ENST00000513189.1 | c.39C>T | p.Gly13= | synonymous_variant | 2/5 | 1 | |||
TLR3 | ENST00000698351.1 | c.39C>T | p.Gly13= | synonymous_variant | 2/5 | ||||
TLR3 | ENST00000698352.1 | c.39C>T | p.Gly13= | synonymous_variant, NMD_transcript_variant | 2/5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251422Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135884
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727246
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74402
ClinVar
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at