Genetic Variant NM_003352.8:c.87+2513A>G (chr2-202217519-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003352.8(SUMO1):c.87+2513A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,772 control chromosomes in the GnomAD database, including 6,133 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 0.27 ( 6133 hom., cov: 30)

Consequence

SUMO1
NM_003352.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.820

Publications

6 publications found

Variant links:

Genes affected

SUMO1 (HGNC:12502): (small ubiquitin like modifier 1) 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 four amino acids of the carboxy-terminus have been cleaved off. Several pseudogenes have been reported for this gene. Alternate transcriptional splice variants encoding different isoforms have been characterized. [provided by RefSeq, Jul 2008]

SUMO1 Gene-Disease associations (from GenCC):

orofacial cleft 10
Inheritance: AD, Unknown Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)

SUMO1 links:

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new If you want to explore the variant's impact on the transcript NM_003352.8, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003352.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SUMO1	NM_003352.8	MANE Select	c.87+2513A>G	intron	N/A	NP_003343.1	P63165-1
SUMO1	NM_001371394.1		c.87+2513A>G	intron	N/A	NP_001358323.1	B8ZZN6
SUMO1	NM_001005781.2		c.87+2513A>G	intron	N/A	NP_001005781.1	P63165-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SUMO1	ENST00000392246.7	TSL:1 MANE Select	c.87+2513A>G	intron	N/A	ENSP00000376077.2	P63165-1
SUMO1	ENST00000409498.6	TSL:3	c.-31+2513A>G	intron	N/A	ENSP00000386472.2	B8ZZ67
SUMO1	ENST00000409368.5	TSL:4	c.87+2513A>G	intron	N/A	ENSP00000387204.1	B8ZZN6

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40383

AN:

151654

Hom.:

6131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.379

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.341

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.295

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

GnomAD4 genome

AF:

0.266

AC:

40376

AN:

151772

Hom.:

6133

Cov.:

AF XY:

0.267

AC XY:

19813

AN XY:

74154

show subpopulations

African (AFR)

AF:

0.108

AC:

4470

AN:

41440

American (AMR)

AF:

0.252

AC:

3826

AN:

15178

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

1314

AN:

3470

East Asian (EAS)

AF:

0.295

AC:

1519

AN:

5148

South Asian (SAS)

AF:

0.342

AC:

1644

AN:

4814

European-Finnish (FIN)

AF:

0.317

AC:

3332

AN:

10510

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.344

AC:

23336

AN:

67908

Other (OTH)

AF:

0.292

AC:

613

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1430

2860

4291

5721

7151

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

436

872

1308

1744

2180

<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:

0.209

Hom.:

601

Bravo

AF:

0.252

Asia WGS

AF:

0.326

AC:

1133

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.93

(source)

DANN

Benign

0.63

PhyloP100

-0.82

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over