rs2305653
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001211.6(BUB1B):c.1568-108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 929,006 control chromosomes in the GnomAD database, including 135,885 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.54 ( 22827 hom., cov: 30)
Exomes 𝑓: 0.53 ( 113058 hom. )
Consequence
BUB1B
NM_001211.6 intron
NM_001211.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.28
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant 15-40202297-G-A is Benign according to our data. Variant chr15-40202297-G-A is described in ClinVar as [Benign]. Clinvar id is 1276830.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUB1B | NM_001211.6 | c.1568-108G>A | intron_variant | ENST00000287598.11 | |||
LOC107984763 | XR_001751506.2 | n.218-22096C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUB1B | ENST00000287598.11 | c.1568-108G>A | intron_variant | 1 | NM_001211.6 | P1 | |||
BUB1B | ENST00000412359.7 | c.1610-108G>A | intron_variant | 2 | |||||
BUB1B | ENST00000559733.5 | c.*481-108G>A | intron_variant, NMD_transcript_variant | 3 | |||||
BUB1B | ENST00000558972.1 | n.373-108G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.544 AC: 82418AN: 151612Hom.: 22793 Cov.: 30
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GnomAD4 exome AF: 0.534 AC: 415061AN: 777278Hom.: 113058 AF XY: 0.533 AC XY: 217224AN XY: 407510
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GnomAD4 genome ? AF: 0.544 AC: 82510AN: 151728Hom.: 22827 Cov.: 30 AF XY: 0.540 AC XY: 40056AN XY: 74144
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 10, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at