chr19-4816305-C-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_182919.4(TICAM1):c.2073G>T(p.Leu691=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TICAM1
NM_182919.4 synonymous
NM_182919.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.216
Genes affected
TICAM1 (HGNC:18348): (TIR domain containing adaptor molecule 1) This gene encodes an adaptor protein containing a Toll/interleukin-1 receptor (TIR) homology domain, which is an intracellular signaling domain that mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. This protein is involved in native immunity against invading pathogens. It specifically interacts with toll-like receptor 3, but not with other TLRs, and this association mediates dsRNA induction of interferon-beta through activation of nuclear factor kappa-B, during an antiviral immune response. Mutations in this gene are associated with encephalopathy, acute, infection-induced. [provided by RefSeq, Jul 2020]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 19-4816305-C-A is Benign according to our data. Variant chr19-4816305-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1561510.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.216 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| TICAM1 | NM_182919.4 | c.2073G>T | p.Leu691= | synonymous_variant | 2/2 | ENST00000248244.6 | |
| TICAM1 | NM_001385678.1 | c.2031G>T | p.Leu677= | synonymous_variant | 3/3 | ||
| TICAM1 | NM_001385679.1 | c.1938G>T | p.Leu646= | synonymous_variant | 2/2 | ||
| TICAM1 | NM_001385680.1 | c.1431G>T | p.Leu477= | synonymous_variant | 3/3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TICAM1 | ENST00000248244.6 | c.2073G>T | p.Leu691= | synonymous_variant | 2/2 | 1 | NM_182919.4 | P1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1375070Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 675060
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
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0
AN:
1375070
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Cov.:
36
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0
AN XY:
675060
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 4 Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 09, 2022 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.