rs4926670

Positions:

• chr1-55197007-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015306.3(USP24):​c.324+17783G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,292 control chromosomes in the GnomAD database, including 644 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 0.073 (644 hom., cov: 32)
• Consequence: USP24 NM_015306.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USP24	NM_015306.3	c.324+17783G>A		intron_variant		ENST00000294383.7	NP_056121.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USP24	ENST00000294383.7	c.324+17783G>A		intron_variant		5	NM_015306.3	ENSP00000294383	P1
USP24	ENST00000484447.6	c.324+17783G>A		intron_variant		3		ENSP00000489026

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11066 AN: 152172 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0572

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.0583

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0727 AC: 11072 AN: 152292 Hom.: 644 Cov.: 32 AF XY: 0.0804 AC XY: 5982 AN XY: 74442

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0573

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.0843

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0847 Hom.: 287

Bravo AF: 0.0544

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.28

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

Other links and lift over

dbSNP: rs4926670; hg19: chr1-55662680;