chr15-40161179-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001211.6(BUB1B):c.-42A>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 0.0122 in 1,609,880 control chromosomes in the GnomAD database, including 168 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 14 hom., cov: 32)
Exomes 𝑓: 0.012 ( 154 hom. )
Consequence
BUB1B
NM_001211.6 5_prime_UTR
NM_001211.6 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.156
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=-0.82).
BP6
?
Variant 15-40161179-A-G is Benign according to our data. Variant chr15-40161179-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1211774.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0102 (1552/152254) while in subpopulation NFE AF= 0.0142 (968/68012). AF 95% confidence interval is 0.0135. There are 14 homozygotes in gnomad4. There are 784 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 14 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUB1B | NM_001211.6 | c.-42A>G | 5_prime_UTR_variant | 1/23 | ENST00000287598.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUB1B | ENST00000287598.11 | c.-42A>G | 5_prime_UTR_variant | 1/23 | 1 | NM_001211.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0102 AC: 1552AN: 152136Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.00999 AC: 2420AN: 242150Hom.: 17 AF XY: 0.00965 AC XY: 1266AN XY: 131198
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GnomAD4 exome AF: 0.0124 AC: 18140AN: 1457626Hom.: 154 Cov.: 31 AF XY: 0.0122 AC XY: 8820AN XY: 724724
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GnomAD4 genome ? AF: 0.0102 AC: 1552AN: 152254Hom.: 14 Cov.: 32 AF XY: 0.0105 AC XY: 784AN XY: 74442
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2019 | - - |
Computational scores
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Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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