rs146387899
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_001211.6(BUB1B):c.772C>T(p.Leu258Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,613,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001211.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BUB1B | NM_001211.6 | c.772C>T | p.Leu258Phe | missense_variant | 7/23 | ENST00000287598.11 | NP_001202.5 | |
LOC107984763 | XR_001751506.2 | n.218-4984G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BUB1B | ENST00000287598.11 | c.772C>T | p.Leu258Phe | missense_variant | 7/23 | 1 | NM_001211.6 | ENSP00000287598.7 | ||
BUB1B | ENST00000412359.7 | c.814C>T | p.Leu272Phe | missense_variant | 7/23 | 2 | ENSP00000398470.3 | |||
BUB1B | ENST00000559461.1 | n.181C>T | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
BUB1B | ENST00000559733.5 | n.169+1302C>T | intron_variant | 3 | ENSP00000453643.1 |
Frequencies
GnomAD3 genomes AF: 0.000769 AC: 117AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251020Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135806
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461790Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727206
GnomAD4 genome AF: 0.000769 AC: 117AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000793 AC XY: 59AN XY: 74390
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 24, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
BUB1B-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 14, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Mosaic variegated aneuploidy syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at