19-4816404-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_182919.4(TICAM1):c.1974G>A(p.Pro658Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,552,574 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P658P) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
TICAM1
NM_182919.4 synonymous
NM_182919.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.44
Publications
0 publications found
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]
TICAM1 Gene-Disease associations (from GenCC):
- herpes simplex encephalitis, susceptibility to, 4Inheritance: AR, SD, AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP7
Synonymous conserved (PhyloP=-4.44 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TICAM1 | NM_182919.4 | c.1974G>A | p.Pro658Pro | synonymous_variant | Exon 2 of 2 | ENST00000248244.6 | NP_891549.1 | |
| TICAM1 | NM_001385678.1 | c.1932G>A | p.Pro644Pro | synonymous_variant | Exon 3 of 3 | NP_001372607.1 | ||
| TICAM1 | NM_001385679.1 | c.1839G>A | p.Pro613Pro | synonymous_variant | Exon 2 of 2 | NP_001372608.1 | ||
| TICAM1 | NM_001385680.1 | c.1332G>A | p.Pro444Pro | synonymous_variant | Exon 3 of 3 | NP_001372609.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.00000678 AC: 1AN: 147562Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
147562
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00000490 AC: 1AN: 204104 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
204104
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000142 AC: 2AN: 1405012Hom.: 0 Cov.: 36 AF XY: 0.00000144 AC XY: 1AN XY: 695326 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1405012
Hom.:
Cov.:
36
AF XY:
AC XY:
1
AN XY:
695326
show subpopulations
African (AFR)
AF:
AC:
1
AN:
31676
American (AMR)
AF:
AC:
0
AN:
36622
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22174
East Asian (EAS)
AF:
AC:
0
AN:
38698
South Asian (SAS)
AF:
AC:
0
AN:
78732
European-Finnish (FIN)
AF:
AC:
0
AN:
49218
Middle Eastern (MID)
AF:
AC:
0
AN:
5364
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1084890
Other (OTH)
AF:
AC:
0
AN:
57638
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000678 AC: 1AN: 147562Hom.: 0 Cov.: 32 AF XY: 0.0000139 AC XY: 1AN XY: 71894 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
147562
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
71894
show subpopulations
African (AFR)
AF:
AC:
1
AN:
39640
American (AMR)
AF:
AC:
0
AN:
14748
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3442
East Asian (EAS)
AF:
AC:
0
AN:
4952
South Asian (SAS)
AF:
AC:
0
AN:
4598
European-Finnish (FIN)
AF:
AC:
0
AN:
9804
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67136
Other (OTH)
AF:
AC:
0
AN:
2044
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.