10-102644797-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_030912.3(TRIM8):c.180C>T(p.Asn60=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Consequence
TRIM8
NM_030912.3 synonymous
NM_030912.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.31
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 10-102644797-C-T is Benign according to our data. Variant chr10-102644797-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1973107.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.31 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TRIM8 | NM_030912.3 | c.180C>T | p.Asn60= | synonymous_variant | 1/6 | ENST00000643721.2 | NP_112174.2 | |
| TRIM8 | NM_001345950.1 | c.180C>T | p.Asn60= | synonymous_variant | 1/5 | NP_001332879.1 | ||
| TRIM8 | NR_144321.1 | n.303C>T | non_coding_transcript_exon_variant | 1/6 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TRIM8 | ENST00000643721.2 | c.180C>T | p.Asn60= | synonymous_variant | 1/6 | NM_030912.3 | ENSP00000496301 | P1 | ||
| TRIM8 | ENST00000302424.12 | c.180C>T | p.Asn60= | synonymous_variant | 1/5 | 1 | ENSP00000302120 | |||
| TRIM8 | ENST00000710327.1 | c.180C>T | p.Asn60= | synonymous_variant | 1/6 | ENSP00000518207 | P1 | |||
| TRIM8 | ENST00000642664.1 | upstream_gene_variant | ENSP00000496615 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33
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GnomAD4 exome Cov.: 32
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GnomAD4 genome 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74378
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 13, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at