rs11674248

chr2-23931322-A-Cchr2-23931322-A-G

Variant summary

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

The ENST00000446425.2(UBXN2A):n.331+3707A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,852 control chromosomes in the GnomAD database, including 22,373 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 0.53 (22373 hom., cov: 31)
• Consequence: UBXN2A ENST00000446425.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

UBXN2A (HGNC:27265): (UBX domain protein 2A) Predicted to enable ubiquitin binding activity. Predicted to be involved in several processes, including autophagosome assembly; nuclear membrane reassembly; and proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to act upstream of or within cellular response to leukemia inhibitory factor; regulation of gene expression; and regulation of protein metabolic process. Predicted to be located in cis-Golgi network and endoplasmic reticulum. Predicted to be active in cytosol and 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBXN2A	XM_005264166.6	c.-15+3707A>C		intron_variant
UBXN2A	XM_005264168.6	c.-152+3707A>C		intron_variant
UBXN2A	XM_011532633.4	c.-138+3707A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBXN2A	ENST00000446425.2	n.331+3707A>C		intron_variant, non_coding_transcript_variant		1
UBXN2A	ENST00000404924.5	c.-138+3707A>C		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80426 AN: 151736 Hom.: 22361 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.530 AC: 80453 AN: 151852 Hom.: 22373 Cov.: 31 AF XY: 0.536 AC XY: 39813 AN XY: 74216

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.574

Alfa AF: 0.557 Hom.: 22221

Bravo AF: 0.531

Asia WGS AF: 0.686 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.2
Dann	Benign	0.43

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: rs11674248; hg19: chr2-24154192;