rs199784356
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_182919.4(TICAM1):āc.1763A>Cā(p.Gln588Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,613,990 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_182919.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TICAM1 | NM_182919.4 | c.1763A>C | p.Gln588Pro | missense_variant | 2/2 | ENST00000248244.6 | |
TICAM1 | NM_001385678.1 | c.1721A>C | p.Gln574Pro | missense_variant | 3/3 | ||
TICAM1 | NM_001385679.1 | c.1628A>C | p.Gln543Pro | missense_variant | 2/2 | ||
TICAM1 | NM_001385680.1 | c.1121A>C | p.Gln374Pro | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TICAM1 | ENST00000248244.6 | c.1763A>C | p.Gln588Pro | missense_variant | 2/2 | 1 | NM_182919.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000256 AC: 39AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000721 AC: 181AN: 251210Hom.: 1 AF XY: 0.000655 AC XY: 89AN XY: 135834
GnomAD4 exome AF: 0.000177 AC: 258AN: 1461678Hom.: 2 Cov.: 41 AF XY: 0.000165 AC XY: 120AN XY: 727130
GnomAD4 genome ? AF: 0.000249 AC: 38AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74492
ClinVar
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at