18-13734511-A-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003799.3(RNMT):āc.465A>Gā(p.Glu155=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,613,718 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 Benign (ā ).
Frequency
Genomes: š 0.000053 ( 0 hom., cov: 32)
Exomes š: 0.00013 ( 0 hom. )
Consequence
RNMT
NM_003799.3 synonymous
NM_003799.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.595
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 made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
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Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 18-13734511-A-G is Benign according to our data. Variant chr18-13734511-A-G is described in ClinVar as [Benign]. Clinvar id is 758114.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=-0.595 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNMT | NM_003799.3 | c.465A>G | p.Glu155= | synonymous_variant | 4/12 | ENST00000383314.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNMT | ENST00000383314.7 | c.465A>G | p.Glu155= | synonymous_variant | 4/12 | 1 | NM_003799.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152222Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000331 AC: 83AN: 251060Hom.: 0 AF XY: 0.000538 AC XY: 73AN XY: 135670
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GnomAD4 exome AF: 0.000132 AC: 193AN: 1461378Hom.: 0 Cov.: 30 AF XY: 0.000208 AC XY: 151AN XY: 726968
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GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.0000939 AC XY: 7AN XY: 74510
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 18, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at