GeneBe

rs2307832

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_015306.3(USP24):​c.3960+204_3960+205del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 35669 hom., cov: 0)

Consequence

USP24
NM_015306.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212
Variant links:
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 -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
USP24NM_015306.3 linkuse as main transcriptc.3960+204_3960+205del intron_variant ENST00000294383.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
USP24ENST00000294383.7 linkuse as main transcriptc.3960+204_3960+205del intron_variant 5 NM_015306.3 P1
USP24ENST00000484447.6 linkuse as main transcriptc.3960+204_3960+205del intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.653
AC:
99098
AN:
151718
Hom.:
35660
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.322
Gnomad AMI
AF:
0.768
Gnomad AMR
AF:
0.813
Gnomad ASJ
AF:
0.728
Gnomad EAS
AF:
0.907
Gnomad SAS
AF:
0.841
Gnomad FIN
AF:
0.769
Gnomad MID
AF:
0.815
Gnomad NFE
AF:
0.760
Gnomad OTH
AF:
0.716
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.653
AC:
99120
AN:
151838
Hom.:
35669
Cov.:
0
AF XY:
0.662
AC XY:
49106
AN XY:
74198
show subpopulations
Gnomad4 AFR
AF:
0.322
Gnomad4 AMR
AF:
0.813
Gnomad4 ASJ
AF:
0.728
Gnomad4 EAS
AF:
0.907
Gnomad4 SAS
AF:
0.841
Gnomad4 FIN
AF:
0.769
Gnomad4 NFE
AF:
0.760
Gnomad4 OTH
AF:
0.720
Alfa
AF:
0.590
Hom.:
2051
Bravo
AF:
0.642
Asia WGS
AF:
0.840
AC:
2922
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2307832; hg19: chr1-55590787; API