chrX-47198858-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003334.4(UBA1):c.56C>T(p.Pro19Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,210,620 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P19P) has been classified as Likely benign.
Frequency
Consequence
NM_003334.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBA1 | NM_003334.4 | c.56C>T | p.Pro19Leu | missense_variant | Exon 2 of 26 | ENST00000335972.11 | NP_003325.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 3AN: 112303Hom.: 0 Cov.: 24 AF XY: 0.0000581 AC XY: 2AN XY: 34453
GnomAD3 exomes AF: 0.0000163 AC: 3AN: 183491Hom.: 0 AF XY: 0.0000294 AC XY: 2AN XY: 67923
GnomAD4 exome AF: 0.00000819 AC: 9AN: 1098264Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363618
GnomAD4 genome AF: 0.0000267 AC: 3AN: 112356Hom.: 0 Cov.: 24 AF XY: 0.0000579 AC XY: 2AN XY: 34516
ClinVar
Submissions by phenotype
Infantile-onset X-linked spinal muscular atrophy Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at