chr11-116762769-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032725.4(BUD13):c.820T>G(p.Leu274Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032725.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUD13 | NM_032725.4 | c.820T>G | p.Leu274Val | missense_variant | 4/10 | ENST00000260210.5 | |
BUD13 | XM_011543035.3 | c.721T>G | p.Leu241Val | missense_variant | 4/10 | ||
BUD13 | NM_001159736.2 | c.634+186T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUD13 | ENST00000260210.5 | c.820T>G | p.Leu274Val | missense_variant | 4/10 | 1 | NM_032725.4 | P2 | |
BUD13 | ENST00000375445.7 | c.634+186T>G | intron_variant | 1 | A2 | ||||
BUD13 | ENST00000419189.1 | c.70T>G | p.Leu24Val | missense_variant, NMD_transcript_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251410Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135870
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461874Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727240
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.820T>G (p.L274V) alteration is located in exon 4 (coding exon 4) of the BUD13 gene. This alteration results from a T to G substitution at nucleotide position 820, causing the leucine (L) at amino acid position 274 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at