rs3793663

chr10-73500425-T-Cchr10-73500425-T-G

Variant summary

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

The NM_001391956.1(USP54):c.4495+230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 152,310 control chromosomes in the GnomAD database, including 615 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 0.069 (615 hom., cov: 32)
• Consequence: USP54 NM_001391956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

USP54 (HGNC:23513): (ubiquitin specific peptidase 54) Predicted to enable thiol-dependent deubiquitinase. Predicted to be involved in protein deubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

PPP3CB-AS1 (HGNC:50750): (PPP3CB antisense RNA 1 (head to head))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USP54	NM_001391956.1	c.4495+230A>G		intron_variant		ENST00000687698.1
PPP3CB-AS1	NR_132103.1	n.501+738T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USP54	ENST00000687698.1	c.4495+230A>G		intron_variant			NM_001391956.1	P3
PPP3CB-AS1	ENST00000600206.5	n.290+738T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0692 AC: 10537 AN: 152192 Hom.: 616 Cov.: 32

Gnomad AFR AF: 0.0436

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0711

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0693 AC: 10548 AN: 152310 Hom.: 615 Cov.: 32 AF XY: 0.0719 AC XY: 5358 AN XY: 74470

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.0712

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.0435

Gnomad4 NFE AF: 0.0592

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0648 Hom.: 252

Bravo AF: 0.0683

Asia WGS AF: 0.233 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
Dann	Benign	0.39

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: rs3793663; hg19: chr10-75260183;