NM_003799.3:c.1380A>G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_003799.3(RNMT):c.1380A>G(p.Glu460Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000212 in 1,412,180 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: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
RNMT
NM_003799.3 synonymous
NM_003799.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.14
Publications
0 publications found
Genes affected
RNMT (HGNC:10075): (RNA guanine-7 methyltransferase) Enables RNA binding activity and mRNA (guanine-N7-)-methyltransferase activity. Involved in 7-methylguanosine mRNA capping. Located in fibrillar center and nucleoplasm. Part of mRNA cap binding activity complex; mRNA cap methyltransferase complex; and receptor complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 18-13754134-A-G is Benign according to our data. Variant chr18-13754134-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 757966.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.14 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003799.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| RNMT | NM_003799.3 | MANE Select | c.1380A>G | p.Glu460Glu | synonymous | Exon 11 of 12 | NP_003790.1 | O43148-1 | |
| RNMT | NM_001308263.2 | c.1380A>G | p.Glu460Glu | synonymous | Exon 11 of 12 | NP_001295192.1 | O43148-2 | ||
| RNMT | NM_001378134.1 | c.1380A>G | p.Glu460Glu | synonymous | Exon 10 of 11 | NP_001365063.1 | O43148-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RNMT | ENST00000383314.7 | TSL:1 MANE Select | c.1380A>G | p.Glu460Glu | synonymous | Exon 11 of 12 | ENSP00000372804.2 | O43148-1 | |
| RNMT | ENST00000543302.6 | TSL:1 | c.1380A>G | p.Glu460Glu | synonymous | Exon 10 of 11 | ENSP00000446426.1 | O43148-1 | |
| RNMT | ENST00000589866.5 | TSL:1 | c.1380A>G | p.Glu460Glu | synonymous | Exon 10 of 11 | ENSP00000466252.1 | O43148-1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000212 AC: 3AN: 1412180Hom.: 0 Cov.: 24 AF XY: 0.00000142 AC XY: 1AN XY: 705304 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
3
AN:
1412180
Hom.:
Cov.:
24
AF XY:
AC XY:
1
AN XY:
705304
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
32460
American (AMR)
AF:
AC:
0
AN:
44254
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25696
East Asian (EAS)
AF:
AC:
0
AN:
39460
South Asian (SAS)
AF:
AC:
1
AN:
84690
European-Finnish (FIN)
AF:
AC:
0
AN:
52690
Middle Eastern (MID)
AF:
AC:
0
AN:
5666
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1068538
Other (OTH)
AF:
AC:
0
AN:
58726
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0225104), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
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
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
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
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
Publications
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