rs12644835
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015271.5(TRIM2):c.220C>T(p.Leu74=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,800 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 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
TRIM2
NM_015271.5 synonymous
NM_015271.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.72
Genes affected
TRIM2 (HGNC:15974): (tripartite motif containing 2) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic filaments. It plays a neuroprotective role and functions as an E3-ubiquitin ligase in proteasome-mediated degradation of target proteins. Mutations in this gene can cause early-onset axonal neuropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 4-153275897-C-T is Benign according to our data. Variant chr4-153275897-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 474602.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.72 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM2 | NM_015271.5 | c.220C>T | p.Leu74= | synonymous_variant | 3/12 | ENST00000338700.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM2 | ENST00000338700.10 | c.220C>T | p.Leu74= | synonymous_variant | 3/12 | 1 | NM_015271.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152234Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250958Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135680
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GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461566Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727078
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GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74374
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Charcot-Marie-Tooth disease type 2R Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 18, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at