rs1024305
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015306.3(USP24):c.927+1354T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 151,870 control chromosomes in the GnomAD database, including 43,043 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 0.74 ( 43043 hom., cov: 31)
Consequence
USP24
NM_015306.3 intron
NM_015306.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.306
Genes affected
USP24 (HGNC:12623): (ubiquitin specific peptidase 24) Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP24 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Mar 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 = 0.939 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP24 | NM_015306.3 | c.927+1354T>C | intron_variant | ENST00000294383.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP24 | ENST00000294383.7 | c.927+1354T>C | intron_variant | 5 | NM_015306.3 | P1 | |||
USP24 | ENST00000484447.6 | c.927+1354T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.742 AC: 112595AN: 151752Hom.: 43024 Cov.: 31
GnomAD3 genomes
?
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112595
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.742 AC: 112653AN: 151870Hom.: 43043 Cov.: 31 AF XY: 0.749 AC XY: 55585AN XY: 74230
GnomAD4 genome
?
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112653
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151870
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31
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55585
AN XY:
74230
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Asia WGS
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3088
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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