Variant chr15-40161106-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001211.6(BUB1B):c.-115A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 1,370,822 control chromosomes in the GnomAD database, including 326,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 37473 hom., cov: 31)

Exomes 𝑓: 0.68 ( 289140 hom. )

Consequence

BUB1B
NM_001211.6 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.465

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:

BUB1B (HGNC:):

BUB1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 15-40161106-A-G is Benign according to our data. Variant chr15-40161106-A-G is described in ClinVar as [Benign]. Clinvar id is 1294017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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.-115A>G		5_prime_UTR_variant	1/23	ENST00000287598.11	NP_001202.5	O60566-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BUB1B	ENST00000287598 linkuse as main transcript	c.-115A>G		5_prime_UTR_variant	1/23	1	NM_001211.6	ENSP00000287598.7		O60566-1
BUB1B	ENST00000412359 linkuse as main transcript	c.-115A>G		5_prime_UTR_variant	1/23	2		ENSP00000398470.3		O60566-3

Frequencies

GnomAD3 genomes

AF:

0.696

AC:

105749

AN:

151926

Hom.:

37437

Cov.:

show subpopulations

Gnomad AFR

AF:

0.764

Gnomad AMI

AF:

0.845

Gnomad AMR

AF:

0.625

Gnomad ASJ

AF:

0.596

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.739

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.707

Gnomad OTH

AF:

0.634

GnomAD4 exome

AF:

0.684

AC:

833242

AN:

1218774

Hom.:

289140

Cov.:

AF XY:

0.680

AC XY:

409646

AN XY:

602562

show subpopulations

Gnomad4 AFR exome

AF:

0.758

Gnomad4 AMR exome

AF:

0.617

Gnomad4 ASJ exome

AF:

0.585

Gnomad4 EAS exome

AF:

0.354

Gnomad4 SAS exome

AF:

0.570

Gnomad4 FIN exome

AF:

0.733

Gnomad4 NFE exome

AF:

0.706

Gnomad4 OTH exome

AF:

0.655

GnomAD4 genome

AF:

0.696

AC:

105853

AN:

152048

Hom.:

37473

Cov.:

AF XY:

0.691

AC XY:

51360

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.763

Gnomad4 AMR

AF:

0.625

Gnomad4 ASJ

AF:

0.596

Gnomad4 EAS

AF:

0.329

Gnomad4 SAS

AF:

0.566

Gnomad4 FIN

AF:

0.739

Gnomad4 NFE

AF:

0.707

Gnomad4 OTH

AF:

0.637

Alfa

AF:

0.697

Hom.:

14295

Bravo

AF:

0.690

Asia WGS

AF:

0.493

AC:

1714

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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	Jan 10, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

DANN

Benign

0.59

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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