chr15-40217503-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001211.6(BUB1B):c.2686G>A(p.Asp896Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,662 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. D896Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_001211.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUB1B | NM_001211.6 | c.2686G>A | p.Asp896Asn | missense_variant | 21/23 | ENST00000287598.11 | |
BUB1B-PAK6 | NM_001128628.3 | c.-365G>A | 5_prime_UTR_variant | 1/11 | |||
LOC107984763 | XR_001751506.2 | n.217+21982C>T | intron_variant, non_coding_transcript_variant | ||||
BUB1B-PAK6 | NM_001128629.3 | c.-282G>A | 5_prime_UTR_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUB1B | ENST00000287598.11 | c.2686G>A | p.Asp896Asn | missense_variant | 21/23 | 1 | NM_001211.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151844Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251464Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135902
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461818Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727208
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151844Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74136
ClinVar
Submissions by phenotype
See cases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Sep 14, 2019 | ACMG classification criteria: PM1, PM2, PP3, BP1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at