rs1046673
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_182919.4(TICAM1):c.*10C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,502,008 control chromosomes in the GnomAD database, including 18,610 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.18 ( 2784 hom., cov: 32)
Exomes 𝑓: 0.15 ( 15826 hom. )
Consequence
TICAM1
NM_182919.4 3_prime_UTR
NM_182919.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.340
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 19-4816229-G-A is Benign according to our data. Variant chr19-4816229-G-A is described in ClinVar as [Benign]. Clinvar id is 403539.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TICAM1 | NM_182919.4 | c.*10C>T | 3_prime_UTR_variant | 2/2 | ENST00000248244.6 | ||
TICAM1 | NM_001385678.1 | c.*10C>T | 3_prime_UTR_variant | 3/3 | |||
TICAM1 | NM_001385679.1 | c.*10C>T | 3_prime_UTR_variant | 2/2 | |||
TICAM1 | NM_001385680.1 | c.*10C>T | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TICAM1 | ENST00000248244.6 | c.*10C>T | 3_prime_UTR_variant | 2/2 | 1 | NM_182919.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.178 AC: 27128AN: 152050Hom.: 2789 Cov.: 32
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GnomAD3 exomes AF: 0.144 AC: 24574AN: 171030Hom.: 2031 AF XY: 0.143 AC XY: 12905AN XY: 90298
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GnomAD4 exome AF: 0.149 AC: 201146AN: 1349840Hom.: 15826 Cov.: 36 AF XY: 0.149 AC XY: 98386AN XY: 660318
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GnomAD4 genome ? AF: 0.178 AC: 27140AN: 152168Hom.: 2784 Cov.: 32 AF XY: 0.174 AC XY: 12941AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
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Name
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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