rs991848363
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002392.6(MDM2):c.56C>A(p.Ala19Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Consequence
MDM2
NM_002392.6 missense
NM_002392.6 missense
Scores
8
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.02
Genes affected
MDM2 (HGNC:6973): (MDM2 proto-oncogene) This gene encodes a nuclear-localized E3 ubiquitin ligase. The encoded protein can promote tumor formation by targeting tumor suppressor proteins, such as p53, for proteasomal degradation. This gene is itself transcriptionally-regulated by p53. Overexpression or amplification of this locus is detected in a variety of different cancers. There is a pseudogene for this gene on chromosome 2. Alternative splicing results in a multitude of transcript variants, many of which may be expressed only in tumor cells. [provided by RefSeq, Jun 2013]
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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=0.20506397).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T;T;T;D;T;.;.;.;.;T;.;.;.;.;.;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;D;D;D;D;D;D;.;.;.;D;D;D;.;D;D;.;.
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;.;.;L;.;.;.;.;.;.;L;L;.;.;L;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N;N;N;N;N;N;N;D;N;N;N;N;D;N;N;N;D
REVEL
Benign
Sift
Benign
.;T;T;D;D;D;D;D;.;D;D;D;T;D;D;T;D;T;.
Sift4G
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;T;D;D;D
Polyphen
D;.;P;P;P;.;.;.;.;.;P;D;D;P;.;P;.;.;.
Vest4
MutPred
0.33
.;Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);.;Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);Gain of catalytic residue at V8 (P = 0.0195);.;.;
MVP
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.