rs11466719
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_182919.4(TICAM1):c.223C>T(p.Arg75Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00094 in 1,609,320 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R75S) has been classified as Uncertain significance.
Frequency
Consequence
NM_182919.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TICAM1 | NM_182919.4 | c.223C>T | p.Arg75Cys | missense_variant | 2/2 | ENST00000248244.6 | |
TICAM1 | NM_001385678.1 | c.181C>T | p.Arg61Cys | missense_variant | 3/3 | ||
TICAM1 | NM_001385679.1 | c.88C>T | p.Arg30Cys | missense_variant | 2/2 | ||
TICAM1 | NM_001385680.1 | c.-72+229C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TICAM1 | ENST00000248244.6 | c.223C>T | p.Arg75Cys | missense_variant | 2/2 | 1 | NM_182919.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00430 AC: 655AN: 152220Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00112 AC: 267AN: 238856Hom.: 1 AF XY: 0.000864 AC XY: 113AN XY: 130838
GnomAD4 exome AF: 0.000586 AC: 854AN: 1456982Hom.: 4 Cov.: 81 AF XY: 0.000486 AC XY: 352AN XY: 724994
GnomAD4 genome ? AF: 0.00433 AC: 659AN: 152338Hom.: 4 Cov.: 32 AF XY: 0.00443 AC XY: 330AN XY: 74484
ClinVar
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at