rs7983138

Variant names:

• chr13-30657376-C-T
• rs7983138
• NM_005800.5:c.1397-98C>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.1397-98C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 1,208,444 control chromosomes in the GnomAD database, including 113,415 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 0.50 (21520 hom., cov: 32)
  • Exomes 𝑓: 0.41 (91895 hom.)
• Consequence: USPL1 NM_005800.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 8 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USPL1	NM_005800.5	c.1397-98C>T		intron_variant	Intron 8 of 8	ENST00000255304.9	NP_005791.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USPL1	ENST00000255304.9	c.1397-98C>T		intron_variant	Intron 8 of 8	1	NM_005800.5	ENSP00000255304.4
USPL1	ENST00000614860.1	c.410-98C>T		intron_variant	Intron 6 of 6	1		ENSP00000480656.1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75781 AN: 151884 Hom.: 21472 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.497

GnomAD4 exome AF: 0.407 AC: 430404 AN: 1056442 Hom.: 91895 AF XY: 0.410 AC XY: 214715 AN XY: 524120

African (AFR) AF: 0.791 AC: 18698 AN: 23626

American (AMR) AF: 0.387 AC: 7985 AN: 20618

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 7449 AN: 17666

East Asian (EAS) AF: 0.169 AC: 5859 AN: 34766

South Asian (SAS) AF: 0.481 AC: 26994 AN: 56148

European-Finnish (FIN) AF: 0.303 AC: 13930 AN: 45952

Middle Eastern (MID) AF: 0.565 AC: 2712 AN: 4798

European-Non Finnish (NFE) AF: 0.405 AC: 327017 AN: 807146

Other (OTH) AF: 0.432 AC: 19760 AN: 45722

GnomAD4 genome AF: 0.499 AC: 75875 AN: 152002 Hom.: 21520 Cov.: 32 AF XY: 0.491 AC XY: 36477 AN XY: 74284

African (AFR) AF: 0.775 AC: 32154 AN: 41470

American (AMR) AF: 0.438 AC: 6687 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1453 AN: 3472

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

South Asian (SAS) AF: 0.467 AC: 2252 AN: 4822

European-Finnish (FIN) AF: 0.303 AC: 3190 AN: 10540

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27683 AN: 67946

Other (OTH) AF: 0.494 AC: 1042 AN: 2108

Alfa AF: 0.475 Hom.: 3111

Bravo AF: 0.521

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.71
PhyloP100		-0.17
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: rs7983138; hg19: chr13-31231513; COSMIC: COSV55000229;