rs1047130

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001211.6(BUB1B):c.1164G>A(p.Ala388Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,613,594 control chromosomes in the GnomAD database, including 72,408 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A388A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.23 ( 4968 hom., cov: 32)

Exomes 𝑓: 0.30 ( 67440 hom. )

Consequence

BUB1B
NM_001211.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.553

Publications

27 publications found

Variant links:

Genes affected

BUB1B (HGNC:1149): (BUB1 mitotic checkpoint serine/threonine kinase B) This gene encodes a kinase involved in spindle checkpoint function. The protein has been localized to the kinetochore and plays a role in the inhibition of the anaphase-promoting complex/cyclosome (APC/C), delaying the onset of anaphase and ensuring proper chromosome segregation. Impaired spindle checkpoint function has been found in many forms of cancer. [provided by RefSeq, Jul 2008]

BUB1B Gene-Disease associations (from GenCC):

mosaic variegated aneuploidy syndrome 1
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, ClinGen, G2P
rhabdomyosarcoma
Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
mosaic variegated aneuploidy syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

BUB1B links:

LOC107984763 (HGNC:):

LOC107984763 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 15-40196650-G-A is Benign according to our data. Variant chr15-40196650-G-A is described in ClinVar as Benign. ClinVar VariationId is 257632.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.553 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BUB1B	NM_001211.6 link	c.1164G>A	p.Ala388Ala	synonymous_variant	Exon 9 of 23	ENST00000287598.11	NP_001202.5	O60566-1
LOC107984763	XR_001751506.2 link	n.218-16449C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BUB1B	ENST00000287598.11 link	c.1164G>A	p.Ala388Ala	synonymous_variant	Exon 9 of 23	1	NM_001211.6	ENSP00000287598.7		O60566-1
BUB1B	ENST00000412359.7 link	c.1206G>A	p.Ala402Ala	synonymous_variant	Exon 9 of 23	2		ENSP00000398470.3		O60566-3

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34970

AN:

151956

Hom.:

4962

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0613

Gnomad AMI

AF:

0.490

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.279

Gnomad MID

AF:

0.201

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.224

GnomAD2 exomes

AF:

0.272

AC:

68292

AN:

251252

AF XY:

0.273

show subpopulations

Gnomad AFR exome

AF:

0.0594

Gnomad AMR exome

AF:

0.352

Gnomad ASJ exome

AF:

0.185

Gnomad EAS exome

AF:

0.146

Gnomad FIN exome

AF:

0.285

Gnomad NFE exome

AF:

0.313

Gnomad OTH exome

AF:

0.261

GnomAD4 exome

AF:

0.298

AC:

436060

AN:

1461518

Hom.:

67440

Cov.:

AF XY:

0.297

AC XY:

216066

AN XY:

727070

show subpopulations

African (AFR)

AF:

0.0514

AC:

1719

AN:

33472

American (AMR)

AF:

0.349

AC:

15624

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.183

AC:

4771

AN:

26128

East Asian (EAS)

AF:

0.170

AC:

6753

AN:

39688

South Asian (SAS)

AF:

0.244

AC:

21080

AN:

86254

European-Finnish (FIN)

AF:

0.286

AC:

15278

AN:

53416

Middle Eastern (MID)

AF:

0.190

AC:

1095

AN:

5768

European-Non Finnish (NFE)

AF:

0.318

AC:

353454

AN:

1111690

Other (OTH)

AF:

0.270

AC:

16286

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

16837

33673

50510

67346

84183

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11336

22672

34008

45344

56680

<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:

0.230

AC:

34985

AN:

152076

Hom.:

4968

Cov.:

AF XY:

0.229

AC XY:

17020

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0612

AC:

2541

AN:

41516

American (AMR)

AF:

0.295

AC:

4506

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

651

AN:

3466

East Asian (EAS)

AF:

0.147

AC:

762

AN:

5180

South Asian (SAS)

AF:

0.241

AC:

1159

AN:

4814

European-Finnish (FIN)

AF:

0.279

AC:

2946

AN:

10548

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.315

AC:

21439

AN:

67964

Other (OTH)

AF:

0.224

AC:

473

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1284

2569

3853

5138

6422

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.280

Hom.:

11548

Bravo

AF:

0.225

Asia WGS

AF:

0.168

AC:

586

AN:

3478

EpiCase

AF:

0.303

EpiControl

AF:

0.296

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 02, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Mosaic variegated aneuploidy syndrome 1

Benign:2

Jul 14, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Colorectal cancer

Benign:1

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Premature chromatid separation trait

Benign:1

Feb 01, 2025

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

9.7

(source)

DANN

Benign

0.50

PhyloP100

-0.55

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over