rs4144331
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003141.4(TRIM21):c.*36C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,566,640 control chromosomes in the GnomAD database, including 9,348 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.12 ( 1270 hom., cov: 32)
Exomes 𝑓: 0.10 ( 8078 hom. )
Consequence
TRIM21
NM_003141.4 3_prime_UTR
NM_003141.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
TRIM21 (HGNC:11312): (tripartite motif containing 21) This gene encodes 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 encoded protein is part of the RoSSA ribonucleoprotein, which includes a single polypeptide and one of four small RNA molecules. The RoSSA particle localizes to both the cytoplasm and the nucleus. RoSSA interacts with autoantigens in patients with Sjogren syndrome and systemic lupus erythematosus. Alternatively spliced transcript variants for this gene have been described but the full-length nature of only one has been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM21 | NM_003141.4 | c.*36C>A | 3_prime_UTR_variant | 7/7 | ENST00000254436.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM21 | ENST00000254436.8 | c.*36C>A | 3_prime_UTR_variant | 7/7 | 1 | NM_003141.4 | P1 | ||
TRIM21 | ENST00000533692.1 | c.*83C>A | 3_prime_UTR_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.122 AC: 18572AN: 151976Hom.: 1264 Cov.: 32
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GnomAD3 exomes AF: 0.114 AC: 24560AN: 215920Hom.: 1618 AF XY: 0.115 AC XY: 13391AN XY: 116046
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GnomAD4 exome AF: 0.103 AC: 145007AN: 1414546Hom.: 8078 Cov.: 28 AF XY: 0.104 AC XY: 72703AN XY: 700268
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GnomAD4 genome AF: 0.122 AC: 18591AN: 152094Hom.: 1270 Cov.: 32 AF XY: 0.120 AC XY: 8946AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at