rs11674248

Variant names:

• chr2-23931322-A-C
• rs11674248
• ENST00000446425.2:n.331+3707A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-23931322-A-C
• chr2-23931322-A-G

Variant summary

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

The ENST00000404924.5(UBXN2A):​c.-138+3707A>C variant causes a intron 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 ENST00000404924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000404924.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBXN2A	ENST00000446425.2	TSL:1	n.331+3707A>C		intron	N/A
	UBXN2A	ENST00000404924.5	TSL:2	c.-138+3707A>C		intron	N/A	ENSP00000385525.1	P68543-1
	UBXN2A	ENST00000906993.1		c.-133+3707A>C		intron	N/A	ENSP00000577052.1

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

African (AFR) AF: 0.355 AC: 14693 AN: 41386

American (AMR) AF: 0.667 AC: 10183 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2046 AN: 3468

East Asian (EAS) AF: 0.785 AC: 4053 AN: 5166

South Asian (SAS) AF: 0.635 AC: 3056 AN: 4812

European-Finnish (FIN) AF: 0.547 AC: 5754 AN: 10510

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38673 AN: 67940

Other (OTH) AF: 0.574 AC: 1206 AN: 2102

Alfa AF: 0.539 Hom.: 33672

Bravo AF: 0.531

Asia WGS AF: 0.686 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.43
PhyloP100		-0.27
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11674248;

hg19: chr2-24154192;