rs9913676

Variant names:

• chr17-75170617-A-G
• rs9913676
• NM_006937.4:c.226-2216T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006937.4(SUMO2):​c.226-2216T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,442 control chromosomes in the GnomAD database, including 28,760 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 0.60 (28760 hom., cov: 28)
• Consequence: SUMO2 NM_006937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUMO2	NM_006937.4	c.226-2216T>C		intron_variant	Intron 3 of 3	ENST00000420826.7	NP_008868.3
SUMO2	NM_001005849.2	c.154-2216T>C		intron_variant	Intron 2 of 2		NP_001005849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUMO2	ENST00000420826.7	c.226-2216T>C		intron_variant	Intron 3 of 3	1	NM_006937.4	ENSP00000405965.2
SUMO2	ENST00000314523.7	c.154-2216T>C		intron_variant	Intron 2 of 2	2		ENSP00000400886.2
SUMO2	ENST00000578238.2	c.97-2216T>C		intron_variant	Intron 3 of 3	2		ENSP00000461997.1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91479 AN: 151324 Hom.: 28734 Cov.: 28

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.604 AC: 91546 AN: 151442 Hom.: 28760 Cov.: 28 AF XY: 0.602 AC XY: 44568 AN XY: 73972

African (AFR) AF: 0.467 AC: 19244 AN: 41240

American (AMR) AF: 0.554 AC: 8416 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2237 AN: 3462

East Asian (EAS) AF: 0.318 AC: 1631 AN: 5124

South Asian (SAS) AF: 0.638 AC: 3062 AN: 4800

European-Finnish (FIN) AF: 0.687 AC: 7208 AN: 10494

Middle Eastern (MID) AF: 0.621 AC: 180 AN: 290

European-Non Finnish (NFE) AF: 0.703 AC: 47665 AN: 67838

Other (OTH) AF: 0.596 AC: 1250 AN: 2096

Alfa AF: 0.647 Hom.: 4307

Bravo AF: 0.586

Asia WGS AF: 0.491 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.15
DANN	Benign	0.11
PhyloP100		-3.3
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: rs9913676; hg19: chr17-73166712;