X-47241303-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001371072.1(USP11):c.873C>T(p.Thr291Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000745 in 1,207,823 control chromosomes in the GnomAD database, including 1 homozygotes. There are 45 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000080 ( 1 hom. 44 hem. )
Consequence
USP11
NM_001371072.1 synonymous
NM_001371072.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.53
Genes affected
USP11 (HGNC:12609): (ubiquitin specific peptidase 11) Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. This gene encodes a deubiquitinating enzyme which lies in a gene cluster on chromosome Xp11.23 [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant X-47241303-C-T is Benign according to our data. Variant chrX-47241303-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 739635.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-6.53 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 44 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP11 | NM_001371072.1 | c.873C>T | p.Thr291Thr | synonymous_variant | Exon 8 of 21 | ENST00000377107.7 | NP_001358001.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111502Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33666
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GnomAD3 exomes AF: 0.000117 AC: 21AN: 179045Hom.: 0 AF XY: 0.000157 AC XY: 10AN XY: 63783
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GnomAD4 exome AF: 0.0000803 AC: 88AN: 1096321Hom.: 1 Cov.: 32 AF XY: 0.000122 AC XY: 44AN XY: 361953
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GnomAD4 genome AF: 0.0000179 AC: 2AN: 111502Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33666
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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
Apr 16, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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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