X-47198887-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003334.4(UBA1):c.85G>A(p.Val29Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000165 in 1,210,548 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003334.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBA1 | NM_003334.4 | c.85G>A | p.Val29Met | missense_variant | Exon 2 of 26 | ENST00000335972.11 | NP_003325.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112321Hom.: 0 Cov.: 24 AF XY: 0.0000290 AC XY: 1AN XY: 34485
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098227Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 363581
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112321Hom.: 0 Cov.: 24 AF XY: 0.0000290 AC XY: 1AN XY: 34485
ClinVar
Submissions by phenotype
Infantile-onset X-linked spinal muscular atrophy Uncertain:1
This variant is not present in population databases (ExAC no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with UBA1-related conditions. This sequence change replaces valine with methionine at codon 29 of the UBA1 protein (p.Val29Met). The valine residue is moderately conserved and there is a small physicochemical difference between valine and methionine. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at