rs11617613

Variant names:

• chr13-30641738-G-A
• rs11617613
• NM_005800.5:c.983-890G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-30641738-G-A
• chr13-30641738-G-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.983-890G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,192 control chromosomes in the GnomAD database, including 2,662 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 0.17 (2662 hom., cov: 32)
• Consequence: USPL1 NM_005800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USPL1	NM_005800.5	c.983-890G>A		intron_variant	Intron 5 of 8	ENST00000255304.9	NP_005791.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USPL1	ENST00000255304.9	c.983-890G>A		intron_variant	Intron 5 of 8	1	NM_005800.5	ENSP00000255304.4
USPL1	ENST00000614860.1	c.-5-890G>A		intron_variant	Intron 3 of 6	1		ENSP00000480656.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25279 AN: 152074 Hom.: 2660 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.166 AC: 25280 AN: 152192 Hom.: 2662 Cov.: 32 AF XY: 0.165 AC XY: 12293 AN XY: 74408

African (AFR) AF: 0.0451 AC: 1872 AN: 41540

American (AMR) AF: 0.190 AC: 2905 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.0966 AC: 501 AN: 5188

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10576

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15454 AN: 67978

Other (OTH) AF: 0.193 AC: 409 AN: 2116

Alfa AF: 0.216 Hom.: 5169

Bravo AF: 0.160

Asia WGS AF: 0.180 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.80
PhyloP100		0.13
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: rs11617613; hg19: chr13-31215875;