chr19-34430578-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_005499.3(UBA2):āc.141T>Gā(p.Ile47Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000751 in 1,611,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005499.3 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
UBA2 | NM_005499.3 | c.141T>G | p.Ile47Met | missense_variant, splice_region_variant | 2/17 | ENST00000246548.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBA2 | ENST00000246548.9 | c.141T>G | p.Ile47Met | missense_variant, splice_region_variant | 2/17 | 1 | NM_005499.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000453 AC: 69AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000838 AC: 21AN: 250682Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135470
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1459040Hom.: 0 Cov.: 29 AF XY: 0.0000262 AC XY: 19AN XY: 725812
GnomAD4 genome AF: 0.000453 AC: 69AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74516
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.141T>G (p.I47M) alteration is located in exon 2 (coding exon 2) of the UBA2 gene. This alteration results from a T to G substitution at nucleotide position 141, causing the isoleucine (I) at amino acid position 47 to be replaced by a methionine (M). 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