2-25234288-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_022552.5(DNMT3A):c.2730G>A(p.Ala910=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000103 in 1,461,094 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: 0.000010 ( 0 hom. )
Consequence
DNMT3A
NM_022552.5 synonymous
NM_022552.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.70
Genes affected
DNMT3A (HGNC:2978): (DNA methyltransferase 3 alpha) CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA methyltransferase that is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes to the cytoplasm and nucleus and its expression is developmentally regulated. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
?
Variant 2-25234288-C-T is Benign according to our data. Variant chr2-25234288-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2113930.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNMT3A | NM_022552.5 | c.2730G>A | p.Ala910= | synonymous_variant | 23/23 | ENST00000321117.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNMT3A | ENST00000321117.10 | c.2730G>A | p.Ala910= | synonymous_variant | 23/23 | 1 | NM_022552.5 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250912Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135586
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461094Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726764
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Tatton-Brown-Rahman overgrowth syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at