chr10-129467245-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000306010.8(MGMT):c.30C>T(p.Arg10Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000144 in 1,391,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
MGMT
ENST00000306010.8 synonymous
ENST00000306010.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0680
Publications
0 publications found
Genes affected
MGMT (HGNC:7059): (O-6-methylguanine-DNA methyltransferase) Alkylating agents are potent carcinogens that can result in cell death, mutation and cancer. The protein encoded by this gene is a DNA repair protein that is involved in cellular defense against mutagenesis and toxicity from alkylating agents. The protein catalyzes transfer of methyl groups from O(6)-alkylguanine and other methylated moieties of the DNA to its own molecule, which repairs the toxic lesions. Methylation of the genes promoter has been associated with several cancer types, including colorectal cancer, lung cancer, lymphoma and glioblastoma. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 10-129467245-C-T is Benign according to our data. Variant chr10-129467245-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 742776.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.068 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000306010.8. 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 |
|---|---|---|---|---|---|---|---|---|---|
| MGMT | NM_002412.5 | MANE Select | c.-64C>T | 5_prime_UTR | Exon 1 of 5 | NP_002403.3 | P16455 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MGMT | ENST00000306010.8 | TSL:1 | c.30C>T | p.Arg10Arg | synonymous | Exon 1 of 5 | ENSP00000302111.7 | B4DEE8 | |
| MGMT | ENST00000651593.1 | MANE Select | c.-64C>T | 5_prime_UTR | Exon 1 of 5 | ENSP00000498729.1 | P16455 | ||
| MGMT | ENST00000897068.1 | c.-209C>T | 5_prime_UTR | Exon 1 of 5 | ENSP00000567127.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 0.00000144 AC: 2AN: 1391884Hom.: 0 Cov.: 39 AF XY: 0.00000291 AC XY: 2AN XY: 686846 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1391884
Hom.:
Cov.:
39
AF XY:
AC XY:
2
AN XY:
686846
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30994
American (AMR)
AF:
AC:
0
AN:
35086
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24958
East Asian (EAS)
AF:
AC:
0
AN:
34840
South Asian (SAS)
AF:
AC:
0
AN:
78750
European-Finnish (FIN)
AF:
AC:
0
AN:
46124
Middle Eastern (MID)
AF:
AC:
0
AN:
5668
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1077682
Other (OTH)
AF:
AC:
0
AN:
57782
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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
GnomAD4 genome
Cov.:
34
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational 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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