rs587778147

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001211.6(BUB1B):​c.779A>G​(p.Asn260Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

BUB1B
NM_001211.6 missense

Scores

3
16

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 0.777
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08722839).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BUB1BNM_001211.6 linkc.779A>G p.Asn260Ser missense_variant Exon 7 of 23 ENST00000287598.11 NP_001202.5 O60566-1
LOC107984763XR_001751506.2 linkn.218-4991T>C intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BUB1BENST00000287598.11 linkc.779A>G p.Asn260Ser missense_variant Exon 7 of 23 1 NM_001211.6 ENSP00000287598.7 O60566-1
BUB1BENST00000412359.7 linkc.821A>G p.Asn274Ser missense_variant Exon 7 of 23 2 ENSP00000398470.3 O60566-3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

not specified Other:1
Sep 19, 2013
ITMI
Significance: not provided
Review Status: no classification provided
Collection Method: reference population

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.096
BayesDel_addAF
Benign
-0.30
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
13
DANN
Uncertain
0.98
DEOGEN2
Benign
0.073
T;.
Eigen
Benign
-0.29
Eigen_PC
Benign
-0.19
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Benign
0.64
T;T
M_CAP
Benign
0.0054
T
MetaRNN
Benign
0.087
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.2
M;.
PrimateAI
Benign
0.42
T
PROVEAN
Benign
-0.51
N;N
REVEL
Benign
0.045
Sift
Benign
0.61
T;T
Sift4G
Benign
0.87
T;T
Polyphen
0.34
B;B
Vest4
0.11
MutPred
0.20
Gain of relative solvent accessibility (P = 0.0249);.;
MVP
0.81
MPC
0.16
ClinPred
0.29
T
GERP RS
3.6
Varity_R
0.067
gMVP
0.16

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.

Other links and lift over

dbSNP: rs587778147; hg19: chr15-40477393; API