Variant rs1047130 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001211.6(BUB1B):c.1164G>A(p.Ala388=) 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 (★★).

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:6

Conservation

PhyloP100: -0.553

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 links:

LOC107984763 (HGNC:):

LOC107984763 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 257632.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-40196650-G-A is described in Lovd as [Benign].

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/exons	MANE	Protein	UniProt
BUB1B	NM_001211.6 linkuse as main transcript	c.1164G>A	p.Ala388=	synonymous_variant	9/23	ENST00000287598.11	NP_001202.5
LOC107984763	XR_001751506.2 linkuse as main transcript	n.218-16449C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BUB1B	ENST00000287598.11 linkuse as main transcript	c.1164G>A	p.Ala388=	synonymous_variant	9/23	1	NM_001211.6	ENSP00000287598	P1	O60566-1

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

GnomAD3 exomes

AF:

0.272

AC:

68292

AN:

251252

Hom.:

10213

AF XY:

0.273

AC XY:

37009

AN XY:

135796

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 SAS exome

AF:

0.237

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

Gnomad4 AFR exome

AF:

0.0514

Gnomad4 AMR exome

AF:

0.349

Gnomad4 ASJ exome

AF:

0.183

Gnomad4 EAS exome

AF:

0.170

Gnomad4 SAS exome

AF:

0.244

Gnomad4 FIN exome

AF:

0.286

Gnomad4 NFE exome

AF:

0.318

Gnomad4 OTH exome

AF:

0.270

GnomAD4 genome

AF:

0.230

AC:

34985

AN:

152076

Hom.:

4968

Cov.:

AF XY:

0.229

AC XY:

17020

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0612

Gnomad4 AMR

AF:

0.295

Gnomad4 ASJ

AF:

0.188

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.279

Gnomad4 NFE

AF:

0.315

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.289

Hom.:

8914

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:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 02, 2019	- -

Mosaic variegated aneuploidy syndrome 1

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 14, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Colorectal cancer

Benign:1

Benign, criteria provided, single submitter

clinical testing

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Jul 07, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

9.7

DANN

Benign

0.50

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over