rs1394125

Positions:

• chr15-75866642-G-A
• chr15-75866642-G-T

Variant summary

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

The NM_173469.4(UBE2Q2):​c.388-2309G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,814 control chromosomes in the GnomAD database, including 8,493 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 0.33 (8493 hom., cov: 31)
• Consequence: UBE2Q2 NM_173469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

UBE2Q2 (HGNC:19248): (ubiquitin conjugating enzyme E2 Q2) Enables ubiquitin-protein transferase activity. Involved in protein K48-linked ubiquitination. Predicted to be located in cytosol. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE2Q2	NM_173469.4	c.388-2309G>A		intron_variant		ENST00000267938.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2Q2	ENST00000267938.9	c.388-2309G>A		intron_variant		1	NM_173469.4	P1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49752 AN: 151696 Hom.: 8493 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.328 AC: 49771 AN: 151814 Hom.: 8493 Cov.: 31 AF XY: 0.318 AC XY: 23547 AN XY: 74160

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.343

Alfa AF: 0.347 Hom.: 20749

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1394125; hg19: chr15-76158983;