chr2-110637978-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004336.5(BUB1):c.3244C>A(p.Arg1082Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000744 in 1,344,506 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. R1082C) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUB1 | NM_004336.5 | c.3244C>A | p.Arg1082Ser | missense_variant | 25/25 | ENST00000302759.11 | |
BUB1 | NM_001278616.2 | c.3184C>A | p.Arg1062Ser | missense_variant | 24/24 | ||
BUB1 | NM_001278617.2 | c.3073C>A | p.Arg1025Ser | missense_variant | 24/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUB1 | ENST00000302759.11 | c.3244C>A | p.Arg1082Ser | missense_variant | 25/25 | 1 | NM_004336.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000518 AC: 1AN: 192970Hom.: 0 AF XY: 0.00000945 AC XY: 1AN XY: 105768
GnomAD4 exome AF: 7.44e-7 AC: 1AN: 1344506Hom.: 0 Cov.: 30 AF XY: 0.00000151 AC XY: 1AN XY: 662240
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The p.R1082S variant (also known as c.3244C>A), located in coding exon 25 of the BUB1 gene, results from a C to A substitution at nucleotide position 3244. The arginine at codon 1082 is replaced by serine, an amino acid with dissimilar 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