chr2-202218942-G-A

Position:

• chr2-202218942-G-A

Variant summary

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

The NM_003352.8(SUMO1):​c.87+1090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0569 in 151,946 control chromosomes in the GnomAD database, including 332 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 0.057 (332 hom., cov: 32)
• Consequence: SUMO1 NM_003352.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUMO1	NM_003352.8	c.87+1090C>T		intron_variant		ENST00000392246.7	NP_003343.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUMO1	ENST00000392246.7	c.87+1090C>T		intron_variant		1	NM_003352.8	ENSP00000376077	P1

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8661 AN: 151828 Hom.: 335 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.0723

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0596

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

GnomAD4 genome AF: 0.0569 AC: 8647 AN: 151946 Hom.: 332 Cov.: 32 AF XY: 0.0555 AC XY: 4122 AN XY: 74224

Gnomad4 AFR AF: 0.0170

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.0720

Gnomad4 SAS AF: 0.0990

Gnomad4 FIN AF: 0.0339

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.0575

Alfa AF: 0.0637 Hom.: 48

Bravo AF: 0.0562

Asia WGS AF: 0.0550 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs7580433; hg19: chr2-203083665;