NM_001039591.3:c.96+17dupA
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001039591.3(USP9X):c.96+17dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000167 in 1,196,885 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000089 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 9.2e-7 ( 0 hom. 0 hem. )
Consequence
USP9X
NM_001039591.3 intron
NM_001039591.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.194
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant X-41123740-T-TA is Benign according to our data. Variant chrX-41123740-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 3695884.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 111970Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34136
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GnomAD3 exomes AF: 0.00000586 AC: 1AN: 170785Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 57831
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GnomAD4 exome AF: 9.22e-7 AC: 1AN: 1084915Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 350729
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GnomAD4 genome AF: 0.00000893 AC: 1AN: 111970Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34136
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 16, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at