rs4603405

Variant names:

• chr13-30634462-C-T
• rs4603405
• NM_005800.5:c.868+2988C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005800.5(USPL1):​c.868+2988C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,050 control chromosomes in the GnomAD database, including 11,642 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 0.39 (11642 hom., cov: 32)
• Consequence: USPL1 NM_005800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 5 publications found

Genes affected

USPL1 (HGNC:20294): (ubiquitin specific peptidase like 1) Enables SUMO binding activity and SUMO-specific isopeptidase activity. Involved in several processes, including Cajal body organization; protein desumoylation; and snRNA transcription. Located in Cajal body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USPL1	NM_005800.5	c.868+2988C>T		intron_variant	Intron 4 of 8	ENST00000255304.9	NP_005791.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USPL1	ENST00000255304.9	c.868+2988C>T		intron_variant	Intron 4 of 8	1	NM_005800.5	ENSP00000255304.4
USPL1	ENST00000614860.1	c.-119-3282C>T		intron_variant	Intron 2 of 6	1		ENSP00000480656.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58582 AN: 151930 Hom.: 11637 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.386 AC: 58621 AN: 152050 Hom.: 11642 Cov.: 32 AF XY: 0.381 AC XY: 28338 AN XY: 74330

African (AFR) AF: 0.418 AC: 17331 AN: 41450

American (AMR) AF: 0.379 AC: 5789 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3470

East Asian (EAS) AF: 0.164 AC: 850 AN: 5178

South Asian (SAS) AF: 0.458 AC: 2207 AN: 4824

European-Finnish (FIN) AF: 0.297 AC: 3133 AN: 10564

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26707 AN: 67978

Other (OTH) AF: 0.409 AC: 862 AN: 2110

Alfa AF: 0.402 Hom.: 16626

Bravo AF: 0.391

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.85
PhyloP100		-0.95
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: rs4603405; hg19: chr13-31208599;