chr19-4817908-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000248244.6(TICAM1):c.470C>T(p.Thr157Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000929 in 1,613,792 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. T157T) has been classified as Likely benign.
Frequency
Consequence
ENST00000248244.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TICAM1 | NM_182919.4 | c.470C>T | p.Thr157Met | missense_variant | 2/2 | ENST00000248244.6 | NP_891549.1 | |
TICAM1 | NM_001385678.1 | c.428C>T | p.Thr143Met | missense_variant | 3/3 | NP_001372607.1 | ||
TICAM1 | NM_001385679.1 | c.335C>T | p.Thr112Met | missense_variant | 2/2 | NP_001372608.1 | ||
TICAM1 | NM_001385680.1 | c.-71-102C>T | intron_variant | NP_001372609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TICAM1 | ENST00000248244.6 | c.470C>T | p.Thr157Met | missense_variant | 2/2 | 1 | NM_182919.4 | ENSP00000248244 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000723 AC: 18AN: 249042Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134794
GnomAD4 exome AF: 0.0000862 AC: 126AN: 1461630Hom.: 1 Cov.: 80 AF XY: 0.0000949 AC XY: 69AN XY: 727114
GnomAD4 genome AF: 0.000158 AC: 24AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74338
ClinVar
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 4 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Knight Diagnostic Laboratories, Oregon Health and Sciences University | Jul 29, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 01, 2022 | This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 157 of the TICAM1 protein (p.Thr157Met). This variant is present in population databases (rs770166865, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with TICAM1-related conditions. ClinVar contains an entry for this variant (Variation ID: 577610). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at