15-75892399-C-T

Position:

• chr15-75892399-C-T

Variant summary

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

The NM_173469.4(UBE2Q2):​c.1029+1385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,932 control chromosomes in the GnomAD database, including 3,350 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 0.20 (3350 hom., cov: 32)
• Consequence: UBE2Q2 NM_173469.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

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]

UBE2Q2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2Q2	NM_173469.4	c.1029+1385C>T		intron_variant		ENST00000267938.9	NP_775740.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2Q2	ENST00000267938.9	c.1029+1385C>T		intron_variant		1	NM_173469.4	ENSP00000267938.4

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29962 AN: 151812 Hom.: 3339 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.198 AC: 30007 AN: 151932 Hom.: 3350 Cov.: 32 AF XY: 0.197 AC XY: 14645 AN XY: 74268

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.0999

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.193

Alfa AF: 0.167 Hom.: 2361

Bravo AF: 0.210

Asia WGS AF: 0.171 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.75

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: rs335711; hg19: chr15-76184740;