rs10463
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001039591.3(USP9X):c.*164A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0816 in 636,648 control chromosomes in the GnomAD database, including 1,707 homozygotes. There are 13,354 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.060 ( 216 hom., 1898 hem., cov: 23)
Exomes 𝑓: 0.086 ( 1491 hom. 11456 hem. )
Consequence
USP9X
NM_001039591.3 3_prime_UTR
NM_001039591.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.34
Genes affected
USP9X (HGNC:12632): (ubiquitin specific peptidase 9 X-linked) This gene is a member of the peptidase C19 family and encodes a protein that is similar to ubiquitin-specific proteases. Though this gene is located on the X chromosome, it escapes X-inactivation. Mutations in this gene have been associated with Turner syndrome. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant X-41232688-A-G is Benign according to our data. Variant chrX-41232688-A-G is described in ClinVar as [Benign]. Clinvar id is 1296676.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0904 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP9X | NM_001039591.3 | c.*164A>G | 3_prime_UTR_variant | 45/45 | ENST00000378308.7 | NP_001034680.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP9X | ENST00000378308.7 | c.*164A>G | 3_prime_UTR_variant | 45/45 | 5 | NM_001039591.3 | ENSP00000367558 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0603 AC: 6755AN: 111941Hom.: 216 Cov.: 23 AF XY: 0.0556 AC XY: 1897AN XY: 34117
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GnomAD4 exome AF: 0.0862 AC: 45220AN: 524658Hom.: 1491 Cov.: 8 AF XY: 0.0992 AC XY: 11456AN XY: 115458
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GnomAD4 genome AF: 0.0603 AC: 6755AN: 111990Hom.: 216 Cov.: 23 AF XY: 0.0555 AC XY: 1898AN XY: 34176
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at