rs750473735
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_187841.3(TRIM54):c.513+1delG variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000218 in 1,613,508 control chromosomes in the GnomAD database, including 1 homozygotes. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
TRIM54
NM_187841.3 splice_donor, intron
NM_187841.3 splice_donor, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.86
Genes affected
TRIM54 (HGNC:16008): (tripartite motif containing 54) The protein encoded by this gene contains a RING finger motif and is highly similar to the ring finger proteins RNF28/MURF1 and RNF29/MURF2. In vitro studies demonstrated that this protein, RNF28, and RNF29 form heterodimers, which may be important for the regulation of titin kinase and microtubule-dependent signal pathways in striated muscles. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
Multiple lines of computational evidence support a deleterious effect 2: max_spliceai, phyloP100way_vertebrate [when was below the threshold]
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM54 | ENST00000380075.7 | c.502delG | p.Lys168ValfsTer20 | frameshift_variant | Exon 3 of 9 | 1 | NM_187841.3 | ENSP00000369415.3 | ||
TRIM54 | ENST00000296098.4 | c.502delG | p.Lys168AsnfsTer33 | frameshift_variant | Exon 3 of 10 | 1 | ENSP00000296098.4 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152198Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000260 AC: 65AN: 250030Hom.: 0 AF XY: 0.000229 AC XY: 31AN XY: 135194
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GnomAD4 exome AF: 0.000210 AC: 307AN: 1461310Hom.: 1 Cov.: 32 AF XY: 0.000227 AC XY: 165AN XY: 726928
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GnomAD4 genome AF: 0.000289 AC: 44AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74352
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Aug 01, 2018
CeGaT Center for Human Genetics Tuebingen
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 0
DS_DL_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at