rs10517263

Positions:

• chr4-52632502-G-C

Variant summary

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

The NM_022832.4(USP46):​c.37-1358C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,070 control chromosomes in the GnomAD database, including 1,437 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 0.13 (1437 hom., cov: 31)
• Consequence: USP46 NM_022832.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.794

Genes affected

USP46 (HGNC:20075): (ubiquitin specific peptidase 46) Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP46 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Jun 2009]

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 (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USP46	NM_022832.4	c.37-1358C>G		intron_variant		ENST00000441222.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP46	ENST00000441222.8	c.37-1358C>G		intron_variant		1	NM_022832.4	P1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20427 AN: 151952 Hom.: 1426 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.135 AC: 20483 AN: 152070 Hom.: 1437 Cov.: 31 AF XY: 0.135 AC XY: 10024 AN XY: 74340

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.141

Alfa AF: 0.125 Hom.: 181

Bravo AF: 0.140

Asia WGS AF: 0.126 AC: 439 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	5.4
DANN	Benign	0.55

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: rs10517263; hg19: chr4-53498669;