rs1059273
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014788.4(TRIM14):c.*252C>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 0.237 in 768,634 control chromosomes in the GnomAD database, including 27,874 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 0.29 ( 8084 hom., cov: 32)
Exomes 𝑓: 0.23 ( 19790 hom. )
Consequence
TRIM14
NM_014788.4 3_prime_UTR
NM_014788.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.481
Genes affected
TRIM14 (HGNC:16283): (tripartite motif containing 14) 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 and its function has not been determined. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM14 | NM_014788.4 | c.*252C>A | 3_prime_UTR_variant | 6/6 | ENST00000341469.7 | NP_055603.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM14 | ENST00000341469.7 | c.*252C>A | 3_prime_UTR_variant | 6/6 | 1 | NM_014788.4 | ENSP00000344208.2 | |||
TRIM14 | ENST00000342043.3 | c.*28+224C>A | intron_variant | 1 | ENSP00000343990.3 | |||||
TRIM14 | ENST00000375098.7 | c.*28+224C>A | intron_variant | 2 | ENSP00000364239.3 | |||||
TRIM14 | ENST00000478530.1 | n.560+224C>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.286 AC: 43483AN: 151950Hom.: 8078 Cov.: 32
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GnomAD4 exome AF: 0.225 AC: 138754AN: 616566Hom.: 19790 Cov.: 5 AF XY: 0.237 AC XY: 79552AN XY: 336096
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GnomAD4 genome AF: 0.286 AC: 43515AN: 152068Hom.: 8084 Cov.: 32 AF XY: 0.287 AC XY: 21338AN XY: 74338
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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
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