chr12-68811541-T-C

Variant names:

• chr12-68811541-T-C
• rs1690924
• NM_002392.6:c.100-2013T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002392.6(MDM2):​c.100-2013T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,006 control chromosomes in the GnomAD database, including 12,918 homozygotes. 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: 𝑓 0.41 (12918 hom., cov: 30)
• Consequence: MDM2 NM_002392.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 7 publications found

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]

MDM2 Gene-Disease associations (from GenCC):

• Li-Fraumeni syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• lessel-kubisch syndrome

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002392.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MDM2	NM_002392.6	MANE Select	c.100-2013T>C		intron	N/A	NP_002383.2
	MDM2	NM_001367990.1		c.82-2013T>C		intron	N/A	NP_001354919.1
	MDM2	NM_001145337.3		c.82-2013T>C		intron	N/A	NP_001138809.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MDM2	ENST00000258149.11	TSL:1 MANE Select	c.100-2013T>C		intron	N/A	ENSP00000258149.6
	MDM2	ENST00000539479.6	TSL:1	c.82-2013T>C		intron	N/A	ENSP00000444430.2
	MDM2	ENST00000350057.9	TSL:1	c.81+2249T>C		intron	N/A	ENSP00000266624.9

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61190 AN: 150888 Hom.: 12892 Cov.: 30

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.372

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.406 AC: 61276 AN: 151006 Hom.: 12918 Cov.: 30 AF XY: 0.398 AC XY: 29353 AN XY: 73676

African (AFR) AF: 0.466 AC: 19113 AN: 40990

American (AMR) AF: 0.267 AC: 4052 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1435 AN: 5152

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4820

European-Finnish (FIN) AF: 0.432 AC: 4406 AN: 10192

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28817 AN: 67908

Other (OTH) AF: 0.372 AC: 779 AN: 2094

Alfa AF: 0.410 Hom.: 4383

Bravo AF: 0.399

Asia WGS AF: 0.296 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.39
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1690924; hg19: chr12-69205321;