rs683880

Variant names:

• chr1-55081222-T-A
• rs683880
• NM_015306.3:c.7078+100A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-55081222-T-A
• chr1-55081222-T-C
• chr1-55081222-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015306.3(USP24):​c.7078+100A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: USP24 NM_015306.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 7 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USP24	NM_015306.3	c.7078+100A>T		intron_variant	Intron 59 of 67	ENST00000294383.7	NP_056121.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP24	ENST00000294383.7	c.7078+100A>T		intron_variant	Intron 59 of 67	5	NM_015306.3	ENSP00000294383.5
USP24	ENST00000484447.6	c.7078+100A>T		intron_variant	Intron 59 of 67	3		ENSP00000489026.2
USP24	ENST00000472566.1	n.*165A>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1054456 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 529896

African (AFR) AF: 0.00 AC: 0 AN: 23918

American (AMR) AF: 0.00 AC: 0 AN: 30288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19748

East Asian (EAS) AF: 0.00 AC: 0 AN: 35996

South Asian (SAS) AF: 0.00 AC: 0 AN: 61432

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45702

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4706

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 786872

Other (OTH) AF: 0.00 AC: 0 AN: 45794

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.41
DANN	Benign	0.41
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism

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: rs683880; hg19: chr1-55546895;