Genetic Variant USP24:c.*1976C>G (chr1-55067069-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015306.3(USP24):c.*1976C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,078 control chromosomes in the GnomAD database, including 46,226 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 0.77 ( 46219 hom., cov: 31)

Exomes 𝑓: 0.83 ( 7 hom. )

Consequence

USP24
NM_015306.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.881

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]

USP24 links:

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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=-0.81).

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 rank	MANE	Protein	UniProt
USP24	NM_015306.3 link	c.*1976C>G		3_prime_UTR_variant	Exon 68 of 68	ENST00000294383.7	NP_056121.2	Q9UPU5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP24	ENST00000294383 link	c.*1976C>G		3_prime_UTR_variant	Exon 68 of 68	5	NM_015306.3	ENSP00000294383.5		Q9UPU5

Frequencies

GnomAD3 genomes

AF:

0.775

AC:

117771

AN:

151944

Hom.:

46203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.651

Gnomad AMI

AF:

0.818

Gnomad AMR

AF:

0.860

Gnomad ASJ

AF:

0.784

Gnomad EAS

AF:

0.962

Gnomad SAS

AF:

0.866

Gnomad FIN

AF:

0.826

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.800

Gnomad OTH

AF:

0.804

GnomAD4 exome

AF:

0.833

AC:

AN:

Hom.:

Cov.:

AF XY:

0.833

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.900

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.775

AC:

117834

AN:

152060

Hom.:

46219

Cov.:

AF XY:

0.780

AC XY:

57997

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.651

Gnomad4 AMR

AF:

0.861

Gnomad4 ASJ

AF:

0.784

Gnomad4 EAS

AF:

0.961

Gnomad4 SAS

AF:

0.866

Gnomad4 FIN

AF:

0.826

Gnomad4 NFE

AF:

0.800

Gnomad4 OTH

AF:

0.807

Alfa

AF:

0.719

Hom.:

2239

Bravo

AF:

0.772

Asia WGS

AF:

0.893

AC:

3106

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.68

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over