rs12472035

chr2-202221970-G-Achr2-202221970-G-C

Variant summary

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

The NM_003352.8(SUMO1):c.13-1864C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 152,166 control chromosomes in the GnomAD database, including 911 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 0.095 (911 hom., cov: 32)
  • Exomes 𝑓: 0.091 (0 hom.)
• Consequence: SUMO1 NM_003352.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUMO1	NM_003352.8	c.13-1864C>T		intron_variant		ENST00000392246.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUMO1	ENST00000392246.7	c.13-1864C>T		intron_variant		1	NM_003352.8	P1

Frequencies

GnomAD3 genomes AF: 0.0950 AC: 14441 AN: 152026 Hom.: 913 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.120

GnomAD4 exome AF: 0.0909 AC: 2 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.143 AC XY: 2 AN XY: 14

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0625

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0949 AC: 14431 AN: 152144 Hom.: 911 Cov.: 32 AF XY: 0.0974 AC XY: 7239 AN XY: 74360

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0697

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0775 Hom.: 120

Bravo AF: 0.0917

Asia WGS AF: 0.212 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.28
Dann	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs12472035; hg19: chr2-203086693;