chr12-68841626-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002392.6(MDM2):c.*1777G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 209,294 control chromosomes in the GnomAD database, including 13,628 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 0.35 ( 9809 hom., cov: 32)
Exomes 𝑓: 0.35 ( 3819 hom. )
Consequence
MDM2
NM_002392.6 3_prime_UTR
NM_002392.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.570
Publications
21 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 syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- lessel-kubisch syndromeInheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.347 AC: 52691AN: 151814Hom.: 9805 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
52691
AN:
151814
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: 0.353 AC: 20245AN: 57362Hom.: 3819 Cov.: 0 AF XY: 0.352 AC XY: 9313AN XY: 26484 show subpopulations
GnomAD4 exome
AF:
AC:
20245
AN:
57362
Hom.:
Cov.:
0
AF XY:
AC XY:
9313
AN XY:
26484
show subpopulations
African (AFR)
AF:
AC:
648
AN:
2520
American (AMR)
AF:
AC:
397
AN:
1666
Ashkenazi Jewish (ASJ)
AF:
AC:
900
AN:
3672
East Asian (EAS)
AF:
AC:
2410
AN:
8626
South Asian (SAS)
AF:
AC:
111
AN:
530
European-Finnish (FIN)
AF:
AC:
24
AN:
42
Middle Eastern (MID)
AF:
AC:
94
AN:
368
European-Non Finnish (NFE)
AF:
AC:
14084
AN:
35278
Other (OTH)
AF:
AC:
1577
AN:
4660
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
645
1290
1934
2579
3224
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
54
108
162
216
270
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.347 AC: 52729AN: 151932Hom.: 9809 Cov.: 32 AF XY: 0.344 AC XY: 25568AN XY: 74248 show subpopulations
GnomAD4 genome
AF:
AC:
52729
AN:
151932
Hom.:
Cov.:
32
AF XY:
AC XY:
25568
AN XY:
74248
show subpopulations
African (AFR)
AF:
AC:
10764
AN:
41428
American (AMR)
AF:
AC:
3720
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
906
AN:
3464
East Asian (EAS)
AF:
AC:
1454
AN:
5166
South Asian (SAS)
AF:
AC:
1190
AN:
4818
European-Finnish (FIN)
AF:
AC:
4678
AN:
10522
Middle Eastern (MID)
AF:
AC:
79
AN:
294
European-Non Finnish (NFE)
AF:
AC:
28760
AN:
67952
Other (OTH)
AF:
AC:
705
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1757
3514
5272
7029
8786
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
516
1032
1548
2064
2580
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
985
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
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