chr4-165041160-T-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152620.3(TRIM60):c.1088T>C(p.Ile363Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Consequence
TRIM60
NM_152620.3 missense
NM_152620.3 missense
Scores
14
Clinical Significance
Conservation
PhyloP100: -2.44
Genes affected
TRIM60 (HGNC:21162): (tripartite motif containing 60) The protein encoded by this gene contains a RING finger domain, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. Pseudogenes of this gene are located on more than six chromosomes including chromosome 4. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.03547436).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM60 | NM_152620.3 | c.1088T>C | p.Ile363Thr | missense_variant | 3/3 | ENST00000512596.6 | |
TRIM60 | NM_001258025.2 | c.1088T>C | p.Ile363Thr | missense_variant | 4/4 | ||
TRIM60 | XM_011531683.3 | c.1088T>C | p.Ile363Thr | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM60 | ENST00000512596.6 | c.1088T>C | p.Ile363Thr | missense_variant | 3/3 | 2 | NM_152620.3 | P1 | |
TRIM60 | ENST00000508504.1 | c.1088T>C | p.Ile363Thr | missense_variant | 3/3 | 1 | P1 | ||
TRIM60 | ENST00000341062.6 | c.1088T>C | p.Ile363Thr | missense_variant | 2/2 | 5 | P1 | ||
TRIM60 | ENST00000647760.1 | c.1088T>C | p.Ile363Thr | missense_variant | 4/4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
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
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | The c.1088T>C (p.I363T) alteration is located in exon 3 (coding exon 1) of the TRIM60 gene. This alteration results from a T to C substitution at nucleotide position 1088, causing the isoleucine (I) at amino acid position 363 to be replaced by a threonine (T). 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
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;N
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
Polyphen
B;B;B;B
Vest4
0.035, 0.031, 0.034
MutPred
Loss of stability (P = 0.0277);Loss of stability (P = 0.0277);Loss of stability (P = 0.0277);Loss of stability (P = 0.0277);
MVP
0.030
MPC
0.046
ClinPred
T
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.