rs708078

Variant names:

• chr2-238041102-G-A
• rs708078
• NM_080678.3:c.508-186G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-238041102-G-A
• chr2-238041102-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080678.3(UBE2F):​c.508-186G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,882 control chromosomes in the GnomAD database, including 9,176 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 0.34 (9176 hom., cov: 32)
• Consequence: UBE2F NM_080678.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 10 publications found

Genes affected

UBE2F (HGNC:12480): (ubiquitin conjugating enzyme E2 F (putative)) Enables NEDD8 conjugating enzyme activity. Involved in protein neddylation. Predicted to be located in cytosol. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

UBE2F-SCLY (HGNC:48339): (UBE2F-SCLY readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring UBE2F (ubiquitin-conjugating enzyme E2F) and SCLY (selenocysteine lyase) genes on chromosome 2. The read-through transcript is a candidate for non-sense mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080678.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2F	NM_080678.3	MANE Select	c.508-186G>A		intron	N/A	NP_542409.1	Q969M7-1
	UBE2F	NM_001278305.2		c.508-186G>A		intron	N/A	NP_001265234.1	Q969M7-1
	UBE2F	NM_001278308.2		c.445-186G>A		intron	N/A	NP_001265237.1	Q969M7-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBE2F	ENST00000272930.9	TSL:1 MANE Select	c.508-186G>A		intron	N/A	ENSP00000272930.4	Q969M7-1
	UBE2F-SCLY	ENST00000449191.1	TSL:3	n.346-186G>A		intron	N/A	ENSP00000456827.1	H3BSR4
	UBE2F	ENST00000888993.1		c.553-186G>A		intron	N/A	ENSP00000559052.1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52288 AN: 151764 Hom.: 9173 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.344 AC: 52294 AN: 151882 Hom.: 9176 Cov.: 32 AF XY: 0.348 AC XY: 25827 AN XY: 74212

African (AFR) AF: 0.282 AC: 11660 AN: 41406

American (AMR) AF: 0.323 AC: 4933 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1597 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2631 AN: 5140

South Asian (SAS) AF: 0.388 AC: 1869 AN: 4814

European-Finnish (FIN) AF: 0.385 AC: 4058 AN: 10546

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24308 AN: 67916

Other (OTH) AF: 0.369 AC: 778 AN: 2108

Alfa AF: 0.240 Hom.: 809

Bravo AF: 0.339

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.026
DANN	Benign	0.69
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs708078; hg19: chr2-238949743;