chr16-67155510-AGCGCGGC-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003789.4(TRADD):c.289_295del(p.Ala97CysfsTer38) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
TRADD
NM_003789.4 frameshift
NM_003789.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.95
Genes affected
TRADD (HGNC:12030): (TNFRSF1A associated via death domain) The protein encoded by this gene is a death domain containing adaptor molecule that interacts with TNFRSF1A/TNFR1 and mediates programmed cell death signaling and NF-kappaB activation. This protein binds adaptor protein TRAF2, reduces the recruitment of inhibitor-of-apoptosis proteins (IAPs) by TRAF2, and thus suppresses TRAF2 mediated apoptosis. This protein can also interact with receptor TNFRSF6/FAS and adaptor protein FADD/MORT1, and is involved in the Fas-induced cell death pathway. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRADD | NM_003789.4 | c.289_295del | p.Ala97CysfsTer38 | frameshift_variant | 3/5 | ENST00000345057.9 | |
TRADD | NM_001323552.2 | c.289_295del | p.Ala97CysfsTer38 | frameshift_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRADD | ENST00000345057.9 | c.289_295del | p.Ala97CysfsTer38 | frameshift_variant | 3/5 | 1 | NM_003789.4 | P1 | |
TRADD | ENST00000486556.1 | c.109_115del | p.Ala37CysfsTer38 | frameshift_variant | 1/3 | 2 | |||
TRADD | ENST00000563348.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hepatocellular carcinoma Pathogenic:1
Pathogenic, no assertion criteria provided | research | Arun Kumar Laboratory, Indian Institute of Science | Jun 15, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.