rs937283
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002392.6(MDM2):c.-94A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 1,545,708 control chromosomes in the GnomAD database, including 115,332 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.36 ( 10430 hom., cov: 32)
Exomes 𝑓: 0.38 ( 104902 hom. )
Consequence
MDM2
NM_002392.6 5_prime_UTR
NM_002392.6 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.29
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 12-68808384-A-G is Benign according to our data. Variant chr12-68808384-A-G is described in ClinVar as [Benign]. Clinvar id is 1164286.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MDM2 | NM_002392.6 | c.-94A>G | 5_prime_UTR_variant | 1/11 | ENST00000258149.11 | ||
MDM2 | NM_001145339.2 | c.-94A>G | 5_prime_UTR_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MDM2 | ENST00000258149.11 | c.-94A>G | 5_prime_UTR_variant | 1/11 | 1 | NM_002392.6 |
Frequencies
GnomAD3 genomes ? AF: 0.363 AC: 55187AN: 151902Hom.: 10421 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
55187
AN:
151902
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.382 AC: 532294AN: 1393690Hom.: 104902 Cov.: 22 AF XY: 0.377 AC XY: 262884AN XY: 696746
GnomAD4 exome
AF:
AC:
532294
AN:
1393690
Hom.:
Cov.:
22
AF XY:
AC XY:
262884
AN XY:
696746
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.363 AC: 55242AN: 152018Hom.: 10430 Cov.: 32 AF XY: 0.357 AC XY: 26548AN XY: 74308
GnomAD4 genome
?
AF:
AC:
55242
AN:
152018
Hom.:
Cov.:
32
AF XY:
AC XY:
26548
AN XY:
74308
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
976
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Accelerated tumor formation, susceptibility to Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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