chr10-102644736-G-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030912.3(TRIM8):āc.119G>Cā(p.Gly40Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,460,944 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 Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
TRIM8
NM_030912.3 missense
NM_030912.3 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 3.94
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 Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.26618075).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM8 | NM_030912.3 | c.119G>C | p.Gly40Ala | missense_variant | 1/6 | ENST00000643721.2 | NP_112174.2 | |
TRIM8 | NM_001345950.1 | c.119G>C | p.Gly40Ala | missense_variant | 1/5 | NP_001332879.1 | ||
TRIM8 | NR_144321.1 | n.242G>C | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM8 | ENST00000643721.2 | c.119G>C | p.Gly40Ala | missense_variant | 1/6 | NM_030912.3 | ENSP00000496301 | P1 | ||
TRIM8 | ENST00000302424.12 | c.119G>C | p.Gly40Ala | missense_variant | 1/5 | 1 | ENSP00000302120 | |||
TRIM8 | ENST00000710327.1 | c.119G>C | p.Gly40Ala | missense_variant | 1/6 | ENSP00000518207 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1460944Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726784
GnomAD4 exome
AF:
AC:
1
AN:
1460944
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
726784
Gnomad4 AFR exome
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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
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 12, 2024 | The c.119G>C (p.G40A) alteration is located in exon 1 (coding exon 1) of the TRIM8 gene. This alteration results from a G to C substitution at nucleotide position 119, causing the glycine (G) at amino acid position 40 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;D
REVEL
Benign
Sift
Benign
.;T
Sift4G
Benign
.;T
Polyphen
B;.
Vest4
0.34
MutPred
Loss of ubiquitination at K45 (P = 0.1083);Loss of ubiquitination at K45 (P = 0.1083);
MVP
0.23
MPC
1.2
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.