rs6435133

Positions:

• chr2-202209237-A-C
• chr2-202209237-A-G
• chr2-202209237-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392246.7(SUMO1):​c.237+1498T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 151,328 control chromosomes in the GnomAD database, including 58,519 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 0.88 (58519 hom., cov: 27)
• Consequence: SUMO1 ENST00000392246.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUMO1	NM_003352.8	c.237+1498T>G		intron_variant		ENST00000392246.7	NP_003343.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUMO1	ENST00000392246.7	c.237+1498T>G		intron_variant		1	NM_003352.8	ENSP00000376077	P1

Frequencies

GnomAD3 genomes AF: 0.879 AC: 132870 AN: 151214 Hom.: 58465 Cov.: 27

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.926

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.879 AC: 132981 AN: 151328 Hom.: 58519 Cov.: 27 AF XY: 0.877 AC XY: 64764 AN XY: 73836

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.862

Alfa AF: 0.858 Hom.: 3900

Bravo AF: 0.877

Asia WGS AF: 0.782 AC: 2717 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.088
DANN	Benign	0.18

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

Other links and lift over

dbSNP: rs6435133; hg19: chr2-203073960;