rs3793663

Variant names:

• chr10-73500425-T-C
• rs3793663
• NM_001391956.1:c.4495+230A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-73500425-T-C
• chr10-73500425-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001391956.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP54	NM_001391956.1	MANE Select	c.4495+230A>G		intron	N/A	NP_001378885.1	Q70EL1-1
	USP54	NM_001391941.1		c.4561+230A>G		intron	N/A	NP_001378870.1
	USP54	NM_001391953.1		c.4495+230A>G		intron	N/A	NP_001378882.1	Q70EL1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP54	ENST00000687698.1	MANE Select	c.4495+230A>G		intron	N/A	ENSP00000510226.1	Q70EL1-1
	USP54	ENST00000422491.7	TSL:1	c.*1461-1237A>G		intron	N/A	ENSP00000407368.4	A0A804D9U3
	PPP3CB-AS1	ENST00000422977.3	TSL:1	n.1298+738T>C		intron	N/A

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

African (AFR) AF: 0.0436 AC: 1811 AN: 41560

American (AMR) AF: 0.0712 AC: 1089 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 320 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1547 AN: 5188

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4824

European-Finnish (FIN) AF: 0.0435 AC: 462 AN: 10622

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4029 AN: 68026

Other (OTH) AF: 0.0658 AC: 139 AN: 2112

Alfa AF: 0.0645 Hom.: 268

Bravo AF: 0.0683

Asia WGS AF: 0.233 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.39
PhyloP100		-1.1
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: rs3793663; hg19: chr10-75260183;