dbSNP rs12297820: SENP1:c.1691+36C>T (chr12-48047965-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001267594.2(SENP1):c.1691+36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0887 in 1,376,252 control chromosomes in the GnomAD database, including 6,273 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 0.094 ( 767 hom., cov: 32)

Exomes 𝑓: 0.088 ( 5506 hom. )

Consequence

SENP1
NM_001267594.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0100

Publications

9 publications found

Variant links:

Genes affected

SENP1 (HGNC:17927): (SUMO specific peptidase 1) This gene encodes a cysteine protease that specifically targets members of the small ubiquitin-like modifier (SUMO) protein family. This protease regulates SUMO pathways by deconjugating sumoylated proteins. This protease also functions to process the precursor SUMO proteins into their mature form. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

SENP1 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SENP1	NM_001267594.2 link	c.1691+36C>T		intron_variant	Intron 15 of 17	ENST00000549518.6	NP_001254523.1	Q9P0U3-1Q6N001

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SENP1	ENST00000549518.6 link	c.1691+36C>T	intron_variant	Intron 15 of 17	1	NM_001267594.2	ENSP00000447328.1	Q9P0U3-1
SENP1	ENST00000448372.6 link	c.1691+36C>T	intron_variant	Intron 15 of 17	1		ENSP00000394791.2	Q9P0U3-1
SENP1	ENST00000552189.5 link	n.*1429+36C>T	intron_variant	Intron 16 of 18	1		ENSP00000447593.1	F8W0I8
SENP1	ENST00000549595.5 link	c.1691+36C>T	intron_variant	Intron 14 of 16	5		ENSP00000450076.1	Q9P0U3-2

Frequencies

GnomAD3 genomes

AF:

0.0934

AC:

14190

AN:

151960

Hom.:

762

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0528

Gnomad ASJ

AF:

0.0482

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0164

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0979

Gnomad OTH

AF:

0.0757

GnomAD2 exomes

AF:

0.0720

AC:

17483

AN:

242868

AF XY:

0.0703

show subpopulations

Gnomad AFR exome

AF:

0.120

Gnomad AMR exome

AF:

0.0335

Gnomad ASJ exome

AF:

0.0504

Gnomad EAS exome

AF:

0.000395

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.0965

Gnomad OTH exome

AF:

0.0702

GnomAD4 exome

AF:

0.0881

AC:

107883

AN:

1224174

Hom.:

5506

Cov.:

AF XY:

0.0855

AC XY:

53035

AN XY:

620556

show subpopulations

African (AFR)

AF:

0.119

AC:

3377

AN:

28388

American (AMR)

AF:

0.0350

AC:

1512

AN:

43188

Ashkenazi Jewish (ASJ)

AF:

0.0522

AC:

1277

AN:

24480

East Asian (EAS)

AF:

0.000545

AC:

AN:

38532

South Asian (SAS)

AF:

0.0208

AC:

1663

AN:

80016

European-Finnish (FIN)

AF:

0.112

AC:

5942

AN:

53128

Middle Eastern (MID)

AF:

0.0436

AC:

231

AN:

5296

European-Non Finnish (NFE)

AF:

0.0997

AC:

89613

AN:

898736

Other (OTH)

AF:

0.0810

AC:

4247

AN:

52410

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

4710

9420

14130

18840

23550

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2946

5892

8838

11784

14730

<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:

0.0935

AC:

14220

AN:

152078

Hom.:

767

Cov.:

AF XY:

0.0918

AC XY:

6828

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.123

AC:

5101

AN:

41470

American (AMR)

AF:

0.0528

AC:

807

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0482

AC:

167

AN:

3468

East Asian (EAS)

AF:

0.00116

AC:

AN:

5172

South Asian (SAS)

AF:

0.0166

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.115

AC:

1212

AN:

10574

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0979

AC:

6653

AN:

67968

Other (OTH)

AF:

0.0750

AC:

158

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

645

1290

1935

2580

3225

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.0915

Hom.:

734

Bravo

AF:

0.0892

Asia WGS

AF:

0.0240

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.16

(source)

DANN

Benign

0.48

PhyloP100

-0.010

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over