rs16405
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_033637.4(BTRC):c.*840_*848del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,084 control chromosomes in the GnomAD database, including 9,719 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 9714 hom., cov: 0)
Exomes 𝑓: 0.20 ( 5 hom. )
Consequence
BTRC
NM_033637.4 3_prime_UTR
NM_033637.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.97
Genes affected
BTRC (HGNC:1144): (beta-transducin repeat containing E3 ubiquitin protein ligase) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbws class; in addition to an F-box, this protein contains multiple WD-40 repeats. The encoded protein mediates degradation of CD4 via its interaction with HIV-1 Vpu. It has also been shown to ubiquitinate phosphorylated NFKBIA (nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha), targeting it for degradation and thus activating nuclear factor kappa-B. Alternatively spliced transcript variants have been described. A related pseudogene exists in chromosome 6. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| BTRC | NM_033637.4 | c.*840_*848del | 3_prime_UTR_variant | 15/15 | ENST00000370187.8 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BTRC | ENST00000370187.8 | c.*840_*848del | 3_prime_UTR_variant | 15/15 | 1 | NM_033637.4 | A1 | ||
| BTRC | ENST00000393441.8 | c.*840_*848del | 3_prime_UTR_variant | 14/14 | 1 | ||||
| BTRC | ENST00000408038.6 | c.*840_*848del | 3_prime_UTR_variant | 14/14 | 1 | P4 |
Frequencies
GnomAD3 genomes 0.316 AC: 47959AN: 151688Hom.: 9703 Cov.: 0
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GnomAD4 exome AF: 0.203 AC: 56AN: 276Hom.: 5 AF XY: 0.215 AC XY: 37AN XY: 172
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GnomAD4 genome 0.316 AC: 48008AN: 151808Hom.: 9714 Cov.: 0 AF XY: 0.317 AC XY: 23547AN XY: 74200
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ClinVar
Not reported inComputational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at