rs2307832

Variant names:

• chr1-55125114-CTT-C
• rs2307832
• NM_015306.3:c.3960+204_3960+205delAA

Your query was ambiguous. Multiple possible variants found:

• chr1-55125114-CTT-C
• chr1-55125114-CTT-CT
• chr1-55125114-CTT-CTTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_015306.3(USP24):​c.3960+204_3960+205delAA 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 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 -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 rank	MANE	Protein	UniProt
USP24	NM_015306.3	c.3960+204_3960+205delAA		intron_variant	Intron 34 of 67	ENST00000294383.7	NP_056121.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP24	ENST00000294383.7	c.3960+204_3960+205delAA		intron_variant	Intron 34 of 67	5	NM_015306.3	ENSP00000294383.5
USP24	ENST00000484447.6	c.3960+204_3960+205delAA		intron_variant	Intron 34 of 67	3		ENSP00000489026.2

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99098 AN: 151718 Hom.: 35660 Cov.: 0

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

African (AFR) AF: 0.322 AC: 13323 AN: 41404

American (AMR) AF: 0.813 AC: 12410 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2522 AN: 3466

East Asian (EAS) AF: 0.907 AC: 4677 AN: 5158

South Asian (SAS) AF: 0.841 AC: 4054 AN: 4820

European-Finnish (FIN) AF: 0.769 AC: 8090 AN: 10522

Middle Eastern (MID) AF: 0.812 AC: 237 AN: 292

European-Non Finnish (NFE) AF: 0.760 AC: 51595 AN: 67900

Other (OTH) AF: 0.720 AC: 1516 AN: 2106

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
PhyloP100		0.21
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: rs2307832; hg19: chr1-55590787;