17-75179199-T-C

Variant names:

• chr17-75179199-T-C
• rs35271045
• NM_006937.4:c.153+1858A>G

Variant summary

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

The NM_006937.4(SUMO2):​c.153+1858A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,052 control chromosomes in the GnomAD database, including 6,414 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 0.27 (6414 hom., cov: 32)
• Consequence: SUMO2 NM_006937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUMO2	NM_006937.4	c.153+1858A>G		intron_variant	Intron 2 of 3	ENST00000420826.7	NP_008868.3
SUMO2	NM_001005849.2	c.153+1858A>G		intron_variant	Intron 2 of 2		NP_001005849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUMO2	ENST00000420826.7	c.153+1858A>G		intron_variant	Intron 2 of 3	1	NM_006937.4	ENSP00000405965.2
SUMO2	ENST00000314523.7	c.153+1858A>G		intron_variant	Intron 2 of 2	2		ENSP00000400886.2
SUMO2	ENST00000578238.2	c.24+1858A>G		intron_variant	Intron 2 of 3	2		ENSP00000461997.1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41582 AN: 151934 Hom.: 6414 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.274 AC: 41589 AN: 152052 Hom.: 6414 Cov.: 32 AF XY: 0.276 AC XY: 20524 AN XY: 74330

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.296

Alfa AF: 0.292 Hom.: 6741

Bravo AF: 0.279

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.59

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: rs35271045; hg19: chr17-73175294;