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. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2F	NM_080678.3	c.508-186G>A		intron_variant	Intron 9 of 9	ENST00000272930.9	NP_542409.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2F	ENST00000272930.9	c.508-186G>A		intron_variant	Intron 9 of 9	1	NM_080678.3	ENSP00000272930.4
UBE2F-SCLY	ENST00000449191.1	n.346-186G>A		intron_variant	Intron 6 of 10	3		ENSP00000456827.1

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

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.369

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.026
DANN	Benign	0.69

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: rs708078; hg19: chr2-238949743;