rs9913676
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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
NM_006937.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.31
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 |
---|---|---|---|---|---|---|---|---|
SUMO2 | NM_006937.4 | c.226-2216T>C | intron_variant | ENST00000420826.7 | NP_008868.3 | |||
SUMO2 | NM_001005849.2 | c.154-2216T>C | intron_variant | NP_001005849.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUMO2 | ENST00000420826.7 | c.226-2216T>C | intron_variant | 1 | NM_006937.4 | ENSP00000405965.2 | ||||
SUMO2 | ENST00000314523.7 | c.154-2216T>C | intron_variant | 2 | ENSP00000400886.2 | |||||
SUMO2 | ENST00000578238.2 | c.97-2216T>C | intron_variant | 2 | ENSP00000461997.1 |
Frequencies
GnomAD3 genomes AF: 0.605 AC: 91479AN: 151324Hom.: 28734 Cov.: 28
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.604 AC: 91546AN: 151442Hom.: 28760 Cov.: 28 AF XY: 0.602 AC XY: 44568AN XY: 73972
GnomAD4 genome
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1712
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3478
ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at