NM_016327.3:c.91G>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016327.3(UPB1):c.91G>A(p.Gly31Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000936 in 1,614,082 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_016327.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UPB1 | NM_016327.3 | c.91G>A | p.Gly31Ser | missense_variant | Exon 1 of 10 | ENST00000326010.10 | NP_057411.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UPB1 | ENST00000326010.10 | c.91G>A | p.Gly31Ser | missense_variant | Exon 1 of 10 | 1 | NM_016327.3 | ENSP00000324343.5 | ||
UPB1 | ENST00000382760.2 | c.91G>A | p.Gly31Ser | missense_variant | Exon 1 of 4 | 5 | ENSP00000372208.2 | |||
UPB1 | ENST00000415388.5 | n.91G>A | non_coding_transcript_exon_variant | Exon 1 of 9 | 5 | ENSP00000400684.1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000344 AC: 86AN: 250136Hom.: 1 AF XY: 0.000325 AC XY: 44AN XY: 135346
GnomAD4 exome AF: 0.0000869 AC: 127AN: 1461734Hom.: 1 Cov.: 32 AF XY: 0.0000825 AC XY: 60AN XY: 727166
GnomAD4 genome AF: 0.000158 AC: 24AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74498
ClinVar
Submissions by phenotype
Deficiency of beta-ureidopropionase Uncertain:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
- -
not provided Uncertain:1Benign:1
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at