rs1129352
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001211.6(BUB1B):āc.1623T>Cā(p.Asn541=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00402 in 1,612,164 control chromosomes in the GnomAD database, including 237 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.022 ( 115 hom., cov: 32)
Exomes š: 0.0021 ( 122 hom. )
Consequence
BUB1B
NM_001211.6 synonymous
NM_001211.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.702
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 15-40202460-T-C is Benign according to our data. Variant chr15-40202460-T-C is described in ClinVar as [Benign]. Clinvar id is 257633.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.702 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0751 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUB1B | NM_001211.6 | c.1623T>C | p.Asn541= | synonymous_variant | 13/23 | ENST00000287598.11 | |
LOC107984763 | XR_001751506.2 | n.218-22259A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUB1B | ENST00000287598.11 | c.1623T>C | p.Asn541= | synonymous_variant | 13/23 | 1 | NM_001211.6 | P1 | |
BUB1B | ENST00000412359.7 | c.1665T>C | p.Asn555= | synonymous_variant | 13/23 | 2 | |||
BUB1B | ENST00000558972.1 | n.428T>C | non_coding_transcript_exon_variant | 3/5 | 3 | ||||
BUB1B | ENST00000559733.5 | c.*536T>C | 3_prime_UTR_variant, NMD_transcript_variant | 6/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0220 AC: 3354AN: 152136Hom.: 115 Cov.: 32
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GnomAD3 exomes AF: 0.00549 AC: 1374AN: 250054Hom.: 55 AF XY: 0.00435 AC XY: 588AN XY: 135244
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GnomAD4 exome AF: 0.00214 AC: 3124AN: 1459910Hom.: 122 Cov.: 33 AF XY: 0.00180 AC XY: 1304AN XY: 726296
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GnomAD4 genome ? AF: 0.0221 AC: 3360AN: 152254Hom.: 115 Cov.: 32 AF XY: 0.0214 AC XY: 1594AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
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 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 24, 2019 | - - |
Mosaic variegated aneuploidy syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at