rs9913676

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.31
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
SUMO2NM_006937.4 linkuse as main transcriptc.226-2216T>C intron_variant ENST00000420826.7 NP_008868.3 P61956-1A0A024R8S3
SUMO2NM_001005849.2 linkuse as main transcriptc.154-2216T>C intron_variant NP_001005849.1 P61956-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SUMO2ENST00000420826.7 linkuse as main transcriptc.226-2216T>C intron_variant 1 NM_006937.4 ENSP00000405965.2 P61956-1
SUMO2ENST00000314523.7 linkuse as main transcriptc.154-2216T>C intron_variant 2 ENSP00000400886.2 P61956-2
SUMO2ENST00000578238.2 linkuse as main transcriptc.97-2216T>C intron_variant 2 ENSP00000461997.1 J3KRH1

Frequencies

GnomAD3 genomes
AF:
0.605
AC:
91479
AN:
151324
Hom.:
28734
Cov.:
28
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.467
Gnomad4 AMR
AF:
0.554
Gnomad4 ASJ
AF:
0.646
Gnomad4 EAS
AF:
0.318
Gnomad4 SAS
AF:
0.638
Gnomad4 FIN
AF:
0.687
Gnomad4 NFE
AF:
0.703
Gnomad4 OTH
AF:
0.596
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

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9913676; hg19: chr17-73166712; API