15-40165136-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001211.6(BUB1B):c.119C>T(p.Thr40Met) variant causes a missense change. The variant allele was found at a frequency of 0.0039 in 1,614,136 control chromosomes in the GnomAD database, including 230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T40A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001211.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUB1B | NM_001211.6 | c.119C>T | p.Thr40Met | missense_variant | 2/23 | ENST00000287598.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUB1B | ENST00000287598.11 | c.119C>T | p.Thr40Met | missense_variant | 2/23 | 1 | NM_001211.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0214 AC: 3252AN: 152134Hom.: 113 Cov.: 32
GnomAD3 exomes AF: 0.00532 AC: 1339AN: 251492Hom.: 55 AF XY: 0.00415 AC XY: 564AN XY: 135922
GnomAD4 exome AF: 0.00208 AC: 3043AN: 1461884Hom.: 117 Cov.: 31 AF XY: 0.00174 AC XY: 1262AN XY: 727246
GnomAD4 genome AF: 0.0214 AC: 3258AN: 152252Hom.: 113 Cov.: 32 AF XY: 0.0206 AC XY: 1531AN XY: 74438
ClinVar
Submissions by phenotype
Mosaic variegated aneuploidy syndrome 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not specified Benign:1Other:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 13, 2018 | - - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Carcinoma of colon Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 19, 1998 | - - |
Colorectal cancer;C1850343:Mosaic variegated aneuploidy syndrome 1;C1864389:Premature chromatid separation trait Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 04, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 24, 2019 | This variant is associated with the following publications: (PMID: 28767289, 27331020, 9521327, 24728327) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at