X-47233055-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001371072.1(USP11):​c.12C>T​(p.Val4Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,208,692 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 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 0.000044 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.0000064 ( 0 hom. 4 hem. )

Consequence

USP11
NM_001371072.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0980
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.25).
BP6
Variant X-47233055-C-T is Benign according to our data. Variant chrX-47233055-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2660417.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.098 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 4 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
USP11NM_001371072.1 linkc.12C>T p.Val4Val synonymous_variant Exon 1 of 21 ENST00000377107.7 NP_001358001.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
USP11ENST00000377107.7 linkc.12C>T p.Val4Val synonymous_variant Exon 1 of 21 1 NM_001371072.1 ENSP00000366311.2 G5E9A6
USP11ENST00000218348.7 linkc.141C>T p.Val47Val synonymous_variant Exon 1 of 21 1 ENSP00000218348.3 P51784
USP11ENST00000469080.5 linkn.26C>T non_coding_transcript_exon_variant Exon 1 of 19 1
USP11ENST00000478596.5 linkn.72C>T non_coding_transcript_exon_variant Exon 1 of 4 3

Frequencies

GnomAD3 genomes
AF:
0.0000445
AC:
5
AN:
112364
Hom.:
0
Cov.:
23
AF XY:
0.0000290
AC XY:
1
AN XY:
34520
show subpopulations
Gnomad AFR
AF:
0.000162
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000288
AC:
5
AN:
173648
Hom.:
0
AF XY:
0.0000489
AC XY:
3
AN XY:
61382
show subpopulations
Gnomad AFR exome
AF:
0.0000821
Gnomad AMR exome
AF:
0.000111
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000744
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000638
AC:
7
AN:
1096328
Hom.:
0
Cov.:
31
AF XY:
0.0000111
AC XY:
4
AN XY:
361862
show subpopulations
Gnomad4 AFR exome
AF:
0.0000758
Gnomad4 AMR exome
AF:
0.000114
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000332
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000445
AC:
5
AN:
112364
Hom.:
0
Cov.:
23
AF XY:
0.0000290
AC XY:
1
AN XY:
34520
show subpopulations
Gnomad4 AFR
AF:
0.000162
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000340

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Mar 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

USP11: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.25
CADD
Benign
8.1
DANN
Benign
0.87

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs377322344; hg19: chrX-47092454; API