Genetic Variant UBXN2B:c.84+134G>A (chr8-58411603-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.312

Publications

17 publications found

Variant links:

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]

UBXN2B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001077619.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UBXN2B	NM_001077619.2	MANE Select	c.84+134G>A	intron	N/A	NP_001071087.1
UBXN2B	NM_001363181.1		c.84+134G>A	intron	N/A	NP_001350110.1
UBXN2B	NM_001330535.2		c.84+134G>A	intron	N/A	NP_001317464.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
UBXN2B	ENST00000399598.7	TSL:1 MANE Select	c.84+134G>A	intron	N/A	ENSP00000382507.2
UBXN2B	ENST00000520732.5	TSL:3	n.84+134G>A	intron	N/A	ENSP00000427759.1
UBXN2B	ENST00000522978.1	TSL:3	n.111+134G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45777

AN:

152010

Hom.:

7341

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.221

AC:

2754

AN:

12476

American (AMR)

AF:

0.528

AC:

4043

AN:

7650

Ashkenazi Jewish (ASJ)

AF:

0.186

AC:

2023

AN:

10894

East Asian (EAS)

AF:

0.545

AC:

13020

AN:

23900

South Asian (SAS)

AF:

0.237

AC:

2005

AN:

8470

European-Finnish (FIN)

AF:

0.332

AC:

6958

AN:

20984

Middle Eastern (MID)

AF:

0.179

AC:

335

AN:

1876

European-Non Finnish (NFE)

AF:

0.274

AC:

114604

AN:

417804

Other (OTH)

AF:

0.287

AC:

7288

AN:

25434

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

5334

10668

16002

21336

26670

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3386

6772

10158

13544

16930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.301

AC:

45810

AN:

152126

Hom.:

7351

Cov.:

AF XY:

0.307

AC XY:

22794

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.242

AC:

10062

AN:

41530

American (AMR)

AF:

0.471

AC:

7196

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

674

AN:

3468

East Asian (EAS)

AF:

0.471

AC:

2425

AN:

5152

South Asian (SAS)

AF:

0.282

AC:

1360

AN:

4830

European-Finnish (FIN)

AF:

0.333

AC:

3531

AN:

10590

Middle Eastern (MID)

AF:

0.175

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.288

AC:

19545

AN:

67952

Other (OTH)

AF:

0.306

AC:

645

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1632

3264

4897

6529

8161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.289

Hom.:

23434

Bravo

AF:

0.314

Asia WGS

AF:

0.362

AC:

1257

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.3

(source)

DANN

Benign

0.81

PhyloP100

-0.31

PromoterAI

0.016

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over