rs10483607
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000360392.4(TRIM9):c.*1396T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 985,358 control chromosomes in the GnomAD database, including 1,341 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 0.073 ( 643 hom., cov: 33)
Exomes 𝑓: 0.034 ( 698 hom. )
Consequence
TRIM9
ENST00000360392.4 3_prime_UTR
ENST00000360392.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.32
Genes affected
TRIM9 (HGNC:16288): (tripartite motif containing 9) 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 bodies. Its function has not been identified. Alternate splicing of this gene generates two transcript variants encoding different isoforms. [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=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM9 | NM_001387360.1 | c.1603+1446T>C | intron_variant | ENST00000684578.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM9 | ENST00000360392.4 | c.*1396T>C | 3_prime_UTR_variant | 7/7 | 1 | ||||
TRIM9 | ENST00000684578.1 | c.1603+1446T>C | intron_variant | NM_001387360.1 | |||||
TRIM9 | ENST00000298355.7 | c.1603+1446T>C | intron_variant | 1 | P1 | ||||
TRIM9 | ENST00000338969.9 | c.1591+1446T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0733 AC: 11156AN: 152134Hom.: 644 Cov.: 33
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GnomAD4 exome AF: 0.0341 AC: 28409AN: 833106Hom.: 698 Cov.: 30 AF XY: 0.0338 AC XY: 13006AN XY: 384716
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GnomAD4 genome AF: 0.0733 AC: 11166AN: 152252Hom.: 643 Cov.: 33 AF XY: 0.0759 AC XY: 5654AN XY: 74452
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at