21-15831466-A-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001283041.3(USP25):c.1830A>T(p.Ala610=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 1,613,874 control chromosomes in the GnomAD database, including 8,027 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 0.14 ( 2849 hom., cov: 32)
Exomes 𝑓: 0.062 ( 5178 hom. )
Consequence
USP25
NM_001283041.3 synonymous
NM_001283041.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.19
Genes affected
USP25 (HGNC:12624): (ubiquitin specific peptidase 25) Ubiquitin (MIM 191339) is a highly conserved 76-amino acid protein involved in regulation of intracellular protein breakdown, cell cycle regulation, and stress response. Ubiquitin is released from degraded proteins by disassembly of the polyubiquitin chains, which is mediated by ubiquitin-specific proteases (USPs), such as USP25 (Valero et al., 1999 [PubMed 10644437]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP7
Synonymous conserved (PhyloP=-1.19 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP25 | NM_001283041.3 | c.1830A>T | p.Ala610= | synonymous_variant | 16/26 | ENST00000400183.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP25 | ENST00000400183.7 | c.1830A>T | p.Ala610= | synonymous_variant | 16/26 | 1 | NM_001283041.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.144 AC: 21840AN: 151972Hom.: 2830 Cov.: 32
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GnomAD3 exomes AF: 0.0938 AC: 23581AN: 251322Hom.: 2020 AF XY: 0.0871 AC XY: 11830AN XY: 135828
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GnomAD4 exome AF: 0.0620 AC: 90572AN: 1461782Hom.: 5178 Cov.: 32 AF XY: 0.0621 AC XY: 45166AN XY: 727188
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GnomAD4 genome AF: 0.144 AC: 21909AN: 152092Hom.: 2849 Cov.: 32 AF XY: 0.143 AC XY: 10597AN XY: 74344
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Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at