rs10034164
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022832.4(USP46):c.*4075T>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 0.179 in 152,270 control chromosomes in the GnomAD database, including 3,021 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 0.18 ( 3020 hom., cov: 33)
Exomes 𝑓: 0.13 ( 1 hom. )
Consequence
USP46
NM_022832.4 3_prime_UTR
NM_022832.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.02
Genes affected
USP46 (HGNC:20075): (ubiquitin specific peptidase 46) Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP46 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Jun 2009]
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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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP46 | NM_022832.4 | c.*4075T>C | 3_prime_UTR_variant | 9/9 | ENST00000441222.8 | NP_073743.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP46 | ENST00000441222.8 | c.*4075T>C | 3_prime_UTR_variant | 9/9 | 1 | NM_022832.4 | ENSP00000407818 | P1 |
Frequencies
GnomAD3 genomes AF: 0.179 AC: 27244AN: 152112Hom.: 2995 Cov.: 33
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GnomAD4 exome AF: 0.125 AC: 5AN: 40Hom.: 1 Cov.: 0 AF XY: 0.133 AC XY: 4AN XY: 30
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GnomAD4 genome AF: 0.180 AC: 27327AN: 152230Hom.: 3020 Cov.: 33 AF XY: 0.178 AC XY: 13274AN XY: 74434
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at