10-102644784-ACC-TCT
Position:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_030912.3(TRIM8):c.167_169delinsTCT(p.Asn56_Gln57delinsIleTer) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
TRIM8
NM_030912.3 stop_gained
NM_030912.3 stop_gained
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.22
Genes affected
TRIM8 (HGNC:15579): (tripartite motif containing 8) This gene encodes a member of the tripartite motif (TRIM) protein family. Based on similarities to other proteins, the encoded protein is suspected to be an E3 ubiquitin-protein ligase. Regulation of this gene may be altered in some cancers. Mutations resulting in a truncated protein product have been observed in early-onset epileptic encephalopathy (EOEE). [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM8 | NM_030912.3 | c.167_169delinsTCT | p.Asn56_Gln57delinsIleTer | stop_gained | 1/6 | ENST00000643721.2 | |
TRIM8 | NM_001345950.1 | c.167_169delinsTCT | p.Asn56_Gln57delinsIleTer | stop_gained | 1/5 | ||
TRIM8 | NR_144321.1 | n.290_292delinsTCT | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM8 | ENST00000643721.2 | c.167_169delinsTCT | p.Asn56_Gln57delinsIleTer | stop_gained | 1/6 | NM_030912.3 | P1 | ||
TRIM8 | ENST00000302424.12 | c.167_169delinsTCT | p.Asn56_Gln57delinsIleTer | stop_gained | 1/5 | 1 | |||
TRIM8 | ENST00000710327.1 | c.167_169delinsTCT | p.Asn56_Gln57delinsIleTer | stop_gained | 1/6 | P1 |
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: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Focal segmental glomerulosclerosis and neurodevelopmental syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Sep 24, 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.