NM_015306.3:c.4508+588C>T

Variant names:

• chr1-55120008-G-A
• rs625219
• NM_015306.3:c.4508+588C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015306.3(USP24):​c.4508+588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,168 control chromosomes in the GnomAD database, including 57,396 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 0.87 (57396 hom., cov: 30)
• Consequence: USP24 NM_015306.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP24	NM_015306.3	c.4508+588C>T		intron_variant	Intron 38 of 67	ENST00000294383.7	NP_056121.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP24	ENST00000294383.7	c.4508+588C>T		intron_variant	Intron 38 of 67	5	NM_015306.3	ENSP00000294383.5
USP24	ENST00000484447.6	c.4508+588C>T		intron_variant	Intron 38 of 67	3		ENSP00000489026.2

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131983 AN: 152050 Hom.: 57353 Cov.: 30

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.878

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.868 AC: 132083 AN: 152168 Hom.: 57396 Cov.: 30 AF XY: 0.871 AC XY: 64815 AN XY: 74388

African (AFR) AF: 0.864 AC: 35867 AN: 41496

American (AMR) AF: 0.901 AC: 13773 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2866 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5153 AN: 5178

South Asian (SAS) AF: 0.913 AC: 4402 AN: 4820

European-Finnish (FIN) AF: 0.879 AC: 9301 AN: 10582

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57806 AN: 68018

Other (OTH) AF: 0.880 AC: 1856 AN: 2110

Alfa AF: 0.862 Hom.: 8298

Bravo AF: 0.869

Asia WGS AF: 0.952 AC: 3310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.64
DANN	Benign	0.19
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs625219; hg19: chr1-55585681; COSMIC: COSV53764610;