rs2859998

Variant names:

• chr8-58411603-G-A
• rs2859998
• NM_001077619.2:c.84+134G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-58411603-G-A
• chr8-58411603-G-C
• chr8-58411603-G-T

Variant summary

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

The NM_001077619.2(UBXN2B):​c.84+134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 681,614 control chromosomes in the GnomAD database, including 31,870 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 0.30 (7351 hom., cov: 32)
  • Exomes 𝑓: 0.29 (24519 hom.)
• Consequence: UBXN2B NM_001077619.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

UBXN2B (HGNC:27035): (UBX domain protein 2B) Predicted to enable ubiquitin binding activity. Involved in establishment of mitotic spindle orientation; negative regulation of protein localization to centrosome; and positive regulation of mitotic centrosome separation. Predicted to be located in Golgi apparatus; endoplasmic reticulum; and spindle pole centrosome. 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN2B	NM_001077619.2	c.84+134G>A		intron_variant	Intron 1 of 7	ENST00000399598.7	NP_001071087.1
UBXN2B	NM_001363181.1	c.84+134G>A		intron_variant	Intron 1 of 6		NP_001350110.1
UBXN2B	NM_001330535.2	c.84+134G>A		intron_variant	Intron 1 of 5		NP_001317464.1
UBXN2B	NR_156456.1	n.109+134G>A		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBXN2B	ENST00000399598.7	c.84+134G>A		intron_variant	Intron 1 of 7	1	NM_001077619.2	ENSP00000382507.2
UBXN2B	ENST00000520732.5	n.84+134G>A		intron_variant	Intron 1 of 5	3		ENSP00000427759.1
UBXN2B	ENST00000522978.1	n.111+134G>A		intron_variant	Intron 1 of 6	3
UBXN2B	ENST00000523409.5	n.84+134G>A		intron_variant	Intron 1 of 8	5		ENSP00000428314.1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45777 AN: 152010 Hom.: 7341 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.289 AC: 153030 AN: 529488 Hom.: 24519 AF XY: 0.288 AC XY: 74734 AN XY: 259086

Gnomad4 AFR exome AF: 0.221

Gnomad4 AMR exome AF: 0.528

Gnomad4 ASJ exome AF: 0.186

Gnomad4 EAS exome AF: 0.545

Gnomad4 SAS exome AF: 0.237

Gnomad4 FIN exome AF: 0.332

Gnomad4 NFE exome AF: 0.274

Gnomad4 OTH exome AF: 0.287

GnomAD4 genome AF: 0.301 AC: 45810 AN: 152126 Hom.: 7351 Cov.: 32 AF XY: 0.307 AC XY: 22794 AN XY: 74346

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.306

Alfa AF: 0.280 Hom.: 8060

Bravo AF: 0.314

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.81

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: rs2859998; hg19: chr8-59324162;