Genetic Variant NM_001077619.2: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
UBXN2B	NM_001077619.2 link	c.84+134G>A	intron_variant	Intron 1 of 7	ENST00000399598.7	NP_001071087.1	Q14CS0
UBXN2B	NM_001363181.1 link	c.84+134G>A	intron_variant	Intron 1 of 6		NP_001350110.1
UBXN2B	NM_001330535.2 link	c.84+134G>A	intron_variant	Intron 1 of 5		NP_001317464.1	Q14CS0E5RJ36
UBXN2B	NR_156456.1 link	n.109+134G>A	intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
UBXN2B	ENST00000399598.7 link	c.84+134G>A	intron_variant	Intron 1 of 7	1	NM_001077619.2	ENSP00000382507.2	Q14CS0
UBXN2B	ENST00000520732.5 link	n.84+134G>A	intron_variant	Intron 1 of 5	3		ENSP00000427759.1	E5RGJ4
UBXN2B	ENST00000522978.1 link	n.111+134G>A	intron_variant	Intron 1 of 6	3
UBXN2B	ENST00000523409.5 link	n.84+134G>A	intron_variant	Intron 1 of 8	5		ENSP00000428314.1	E5RJ36

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over