chr2-110637980-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004336.5(BUB1):c.3242A>T(p.Lys1081Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000737 in 1,357,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K1081R) has been classified as Uncertain significance.
Frequency
Consequence
NM_004336.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUB1 | NM_004336.5 | c.3242A>T | p.Lys1081Met | missense_variant | 25/25 | ENST00000302759.11 | |
BUB1 | NM_001278616.2 | c.3182A>T | p.Lys1061Met | missense_variant | 24/24 | ||
BUB1 | NM_001278617.2 | c.3071A>T | p.Lys1024Met | missense_variant | 24/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUB1 | ENST00000302759.11 | c.3242A>T | p.Lys1081Met | missense_variant | 25/25 | 1 | NM_004336.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000506 AC: 1AN: 197712Hom.: 0 AF XY: 0.00000924 AC XY: 1AN XY: 108244
GnomAD4 exome AF: 7.37e-7 AC: 1AN: 1357600Hom.: 0 Cov.: 30 AF XY: 0.00000149 AC XY: 1AN XY: 669578
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2021 | The p.K1081M variant (also known as c.3242A>T), located in coding exon 25 of the BUB1 gene, results from an A to T substitution at nucleotide position 3242. The lysine at codon 1081 is replaced by methionine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at