chr12-109085066-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032663.5(USP30):c.1282G>A(p.Asp428Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000822 in 1,581,386 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000077 ( 0 hom. )
Consequence
USP30
NM_032663.5 missense
NM_032663.5 missense
Scores
1
10
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.53
Genes affected
USP30 (HGNC:20065): (ubiquitin specific peptidase 30) USP30, a member of the ubiquitin-specific protease family (see USP1, MIM 603478), is a novel mitochondrial deubiquitinating (DUB) enzyme (Nakamura and Hirose, 2008 [PubMed 18287522]).[supplied by OMIM, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP30 | NM_032663.5 | c.1282G>A | p.Asp428Asn | missense_variant | 12/13 | ENST00000257548.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP30 | ENST00000257548.10 | c.1282G>A | p.Asp428Asn | missense_variant | 12/13 | 1 | NM_032663.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152094Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000834 AC: 2AN: 239708Hom.: 0 AF XY: 0.00000768 AC XY: 1AN XY: 130226
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GnomAD4 exome AF: 0.00000770 AC: 11AN: 1429292Hom.: 0 Cov.: 31 AF XY: 0.00000705 AC XY: 5AN XY: 709086
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152094Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74286
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Uncertain
D;T
Sift4G
Benign
T;T
Polyphen
D;D
Vest4
MutPred
0.48
.;Gain of catalytic residue at Y429 (P = 2e-04);
MVP
MPC
1.1
ClinPred
D
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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