chr19-4818366-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_182919.4(TICAM1):c.12A>G(p.Thr4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 1,599,354 control chromosomes in the GnomAD database, including 341,718 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T4T) has been classified as Likely benign.
Frequency
Consequence
NM_182919.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TICAM1 | NM_182919.4 | c.12A>G | p.Thr4= | synonymous_variant | 2/2 | ENST00000248244.6 | |
TICAM1 | NM_001385678.1 | c.5-35A>G | intron_variant | ||||
TICAM1 | NM_001385679.1 | c.-89-35A>G | intron_variant | ||||
TICAM1 | NM_001385680.1 | c.-72+18A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TICAM1 | ENST00000248244.6 | c.12A>G | p.Thr4= | synonymous_variant | 2/2 | 1 | NM_182919.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.718 AC: 109257AN: 152068Hom.: 40560 Cov.: 33
GnomAD3 exomes AF: 0.658 AC: 154814AN: 235140Hom.: 51545 AF XY: 0.656 AC XY: 84143AN XY: 128206
GnomAD4 exome AF: 0.642 AC: 929502AN: 1447168Hom.: 301105 Cov.: 63 AF XY: 0.643 AC XY: 462095AN XY: 719048
GnomAD4 genome ? AF: 0.719 AC: 109367AN: 152186Hom.: 40613 Cov.: 33 AF XY: 0.719 AC XY: 53497AN XY: 74386
ClinVar
Submissions by phenotype
not specified Benign:2
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 - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 92% of patients studied by a panel of primary immunodeficiencies. Number of patients: 87. Only high quality variants are reported. - |
Herpes simplex encephalitis, susceptibility to, 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at