rs878853105
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_001039591.3(USP9X):āc.640C>Gā(p.Pro214Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,208,609 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. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_001039591.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP9X | NM_001039591.3 | c.640C>G | p.Pro214Ala | missense_variant | 6/45 | ENST00000378308.7 | NP_001034680.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP9X | ENST00000378308.7 | c.640C>G | p.Pro214Ala | missense_variant | 6/45 | 5 | NM_001039591.3 | ENSP00000367558 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000892 AC: 1AN: 112101Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34251
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1096508Hom.: 0 Cov.: 29 AF XY: 0.00000829 AC XY: 3AN XY: 361910
GnomAD4 genome AF: 0.00000892 AC: 1AN: 112101Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34251
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Clinical Genetics Laboratory, Skane University Hospital Lund | May 27, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 12, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at