chr11-116762786-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032725.4(BUD13):c.803G>A(p.Arg268His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. R268C) has been classified 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BUD13 | NM_032725.4 | c.803G>A | p.Arg268His | missense_variant | 4/10 | ENST00000260210.5 | |
BUD13 | XM_011543035.3 | c.704G>A | p.Arg235His | missense_variant | 4/10 | ||
BUD13 | NM_001159736.2 | c.634+169G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BUD13 | ENST00000260210.5 | c.803G>A | p.Arg268His | missense_variant | 4/10 | 1 | NM_032725.4 | P2 | |
BUD13 | ENST00000375445.7 | c.634+169G>A | intron_variant | 1 | A2 | ||||
BUD13 | ENST00000419189.1 | c.53G>A | p.Arg18His | missense_variant, NMD_transcript_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251424Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135878
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461874Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727236
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at