dbSNP rs7983138: USPL1:c.1397-98C>T (chr13-30657376-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.167

Publications

8 publications found

Variant links:

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]

USPL1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005800.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
USPL1	NM_005800.5	MANE Select	c.1397-98C>T	intron	N/A	NP_005791.3
USPL1	NM_001321532.2		c.854-98C>T	intron	N/A	NP_001308461.1
USPL1	NM_001321533.2		c.410-98C>T	intron	N/A	NP_001308462.1	Q5W0Q7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
USPL1	ENST00000255304.9	TSL:1 MANE Select	c.1397-98C>T	intron	N/A	ENSP00000255304.4	Q5W0Q7-1
USPL1	ENST00000614860.1	TSL:1	c.410-98C>T	intron	N/A	ENSP00000480656.1	Q5W0Q7-2
USPL1	ENST00000898134.1		c.1397-98C>T	intron	N/A	ENSP00000568193.1

Frequencies

GnomAD3 genomes

AF:

0.499

AC:

75781

AN:

151884

Hom.:

21472

Cov.:

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

11844

23688

35531

47375

59219

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9622

19244

28866

38488

48110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.499

AC:

75875

AN:

152002

Hom.:

21520

Cov.:

AF XY:

0.491

AC XY:

36477

AN XY:

74284

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1698

3396

5094

6792

8490

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.8

(source)

DANN

Benign

0.71

PhyloP100

-0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over