Genetic Variant SUMO2:c.-28G>A (chr17-75182862-C-T) – ACMG Classification: Benign (-18 pts)

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_006937.4(SUMO2):c.-28G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00885 in 1,389,238 control chromosomes in the GnomAD database, including 873 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.045 ( 528 hom., cov: 33)

Exomes 𝑓: 0.0044 ( 345 hom. )

Consequence

SUMO2
NM_006937.4 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.58

Publications

0 publications found

Variant links:

Genes affected

SUMO2 (HGNC:11125): (small ubiquitin like modifier 2) This gene encodes a protein that is a member of the SUMO (small ubiquitin-like modifier) protein family. It functions in a manner similar to ubiquitin in that it is bound to target proteins as part of a post-translational modification system. However, unlike ubiquitin which targets proteins for degradation, this protein is involved in a variety of cellular processes, such as nuclear transport, transcriptional regulation, apoptosis, and protein stability. It is not active until the last two amino acids of the carboxy-terminus have been cleaved off. Numerous pseudogenes have been reported for this gene. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

SUMO2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 17-75182862-C-T is Benign according to our data. Variant chr17-75182862-C-T is described in ClinVar as Benign. ClinVar VariationId is 1257423.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006937.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUMO2	NM_006937.4	MANE Select	c.-28G>A		5_prime_UTR	Exon 1 of 4	NP_008868.3
	SUMO2	NM_001005849.2		c.-28G>A		5_prime_UTR	Exon 1 of 3	NP_001005849.1	P61956-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SUMO2	ENST00000420826.7	TSL:1 MANE Select	c.-28G>A	5_prime_UTR	Exon 1 of 4	ENSP00000405965.2	P61956-1
SUMO2	ENST00000919118.1		c.-28G>A	5_prime_UTR	Exon 1 of 5	ENSP00000589177.1
SUMO2	ENST00000919117.1		c.-28G>A	5_prime_UTR	Exon 1 of 4	ENSP00000589176.1

Frequencies

GnomAD3 genomes

AF:

0.0449

AC:

6829

AN:

151930

Hom.:

528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0216

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00100

Gnomad OTH

AF:

0.0364

GnomAD2 exomes

AF:

0.00908

AC:

932

AN:

102644

AF XY:

0.00678

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.0108

Gnomad ASJ exome

AF:

0.00270

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000716

Gnomad OTH exome

AF:

0.00391

GnomAD4 exome

AF:

0.00441

AC:

5459

AN:

1237196

Hom.:

345

Cov.:

AF XY:

0.00393

AC XY:

2386

AN XY:

607018

show subpopulations

African (AFR)

AF:

0.156

AC:

3966

AN:

25412

American (AMR)

AF:

0.0130

AC:

248

AN:

19054

Ashkenazi Jewish (ASJ)

AF:

0.00315

AC:

AN:

18736

East Asian (EAS)

AF:

0.00

AC:

AN:

30006

South Asian (SAS)

AF:

0.000267

AC:

AN:

52372

European-Finnish (FIN)

AF:

0.00

AC:

AN:

43278

Middle Eastern (MID)

AF:

0.0107

AC:

AN:

3370

European-Non Finnish (NFE)

AF:

0.000598

AC:

595

AN:

995808

Other (OTH)

AF:

0.0110

AC:

541

AN:

49160

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

206

413

619

826

1032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

142

284

426

568

710

<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:

0.0450

AC:

6836

AN:

152042

Hom.:

528

Cov.:

AF XY:

0.0433

AC XY:

3217

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.153

AC:

6343

AN:

41494

American (AMR)

AF:

0.0216

AC:

330

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00375

AC:

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5150

South Asian (SAS)

AF:

0.000414

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10554

Middle Eastern (MID)

AF:

0.0137

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00100

AC:

AN:

67958

Other (OTH)

AF:

0.0360

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

289

579

868

1158

1447

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<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:

0.0318

Hom.:

Bravo

AF:

0.0526

Asia WGS

AF:

0.00520

AC:

AN:

3476

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

(source)

DANN

Benign

0.95

PhyloP100

1.6

PromoterAI

0.00060

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

Mutation Taster

=292/8

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