11-11892004-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001282659.2(USP47):āc.394A>Gā(p.Arg132Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
USP47
NM_001282659.2 missense
NM_001282659.2 missense
Scores
3
14
Clinical Significance
Conservation
PhyloP100: 4.30
Genes affected
USP47 (HGNC:20076): (ubiquitin specific peptidase 47) Enables WD40-repeat domain binding activity and thiol-dependent deubiquitinase. Involved in several processes, including monoubiquitinated protein deubiquitination; negative regulation of G2/M transition of mitotic cell cycle; and negative regulation of nitrogen compound metabolic process. Located in cytoplasm. Part of SCF ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]
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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;
BP4
Computational evidence support a benign effect (MetaRNN=0.18784326).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP47 | NM_001282659.2 | c.394A>G | p.Arg132Gly | missense_variant | 4/28 | ENST00000527733.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP47 | ENST00000527733.7 | c.394A>G | p.Arg132Gly | missense_variant | 4/28 | 1 | NM_001282659.2 | P3 | |
USP47 | ENST00000399455.2 | c.454A>G | p.Arg152Gly | missense_variant | 5/29 | 5 | A1 | ||
USP47 | ENST00000339865.9 | c.190A>G | p.Arg64Gly | missense_variant | 3/27 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249238Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135220
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461580Hom.: 0 Cov.: 29 AF XY: 0.00000275 AC XY: 2AN XY: 727066
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ExAC
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.190A>G (p.R64G) alteration is located in exon 3 (coding exon 3) of the USP47 gene. This alteration results from a A to G substitution at nucleotide position 190, causing the arginine (R) at amino acid position 64 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
D;T;T
Sift4G
Benign
T;T;T
Polyphen
B;.;.
Vest4
MutPred
Gain of catalytic residue at F65 (P = 0.0394);.;.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at