12-68809225-A-G

Variant names:

• chr12-68809225-A-G
• rs1880639329
• NM_002392.6:c.32A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002392.6(MDM2):​c.32A>G​(p.Asn11Ser) 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MDM2 NM_002392.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.756

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]

ACMG classification

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=0.10362974).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MDM2	NM_002392.6	c.32A>G	p.Asn11Ser	missense_variant	Exon 2 of 11	ENST00000258149.11	NP_002383.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MDM2	ENST00000258149.11	c.32A>G	p.Asn11Ser	missense_variant	Exon 2 of 11	1	NM_002392.6	ENSP00000258149.6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Accelerated tumor formation, susceptibility to Uncertain:1

Sep 10, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 11 of the MDM2 protein (p.Asn11Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MDM2-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Benign". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.063
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	16
DANN	Uncertain	0.98
DEOGEN2	Benign	0.27	.;T;T;T;T;T;.;.;.;.;T;.;.;.;.;.;T
Eigen	Benign	-0.32
Eigen_PC	Benign	-0.18
FATHMM_MKL	Benign	0.20	N
LIST_S2	Uncertain	0.86	D;D;D;D;T;D;D;D;.;.;.;D;D;D;.;D;D
M_CAP	Benign	0.0052	T
MetaRNN	Benign	0.10	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	.;.;.;.;L;.;.;.;.;.;.;L;L;.;.;L;.
PrimateAI	Benign	0.41	T
PROVEAN	Benign	-1.7	.;N;N;N;N;N;N;N;N;N;N;N;N;N;D;N;N
REVEL	Benign	0.037
Sift	Benign	0.27	.;T;D;D;D;T;T;T;.;T;D;D;D;D;D;D;D
Sift4G	Benign	0.62	T;T;T;T;T;T;T;T;T;T;T;T;T;T;D;T;T
Polyphen		0.0040	B;.;.;B;B;.;.;.;.;.;.;B;.;.;.;.;.
Vest4		0.13
MutPred		0.23		.;Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);.;Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);Gain of catalytic residue at C2 (P = 0.0026);
MVP		0.45
ClinPred		0.091	T
GERP RS		3.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.087
gMVP		0.51

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

Other links and lift over

dbSNP: rs1880639329; hg19: chr12-69203005;