1-20191037-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152376.5(UBXN10):c.476G>A(p.Ser159Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152376.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBXN10 | NM_152376.5 | c.476G>A | p.Ser159Asn | missense_variant | Exon 2 of 2 | ENST00000375099.4 | NP_689589.1 | |
UBXN10 | XM_005245742.5 | c.476G>A | p.Ser159Asn | missense_variant | Exon 2 of 2 | XP_005245799.1 | ||
UBXN10 | XM_011540699.4 | c.476G>A | p.Ser159Asn | missense_variant | Exon 2 of 2 | XP_011539001.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251252Hom.: 1 AF XY: 0.0000515 AC XY: 7AN XY: 135850
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461760Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727174
GnomAD4 genome AF: 0.000276 AC: 42AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.476G>A (p.S159N) alteration is located in exon 2 (coding exon 1) of the UBXN10 gene. This alteration results from a G to A substitution at nucleotide position 476, causing the serine (S) at amino acid position 159 to be replaced by an asparagine (N). 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