rs61758429
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001130823.3(DNMT1):c.687T>G(p.Val229Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,614,066 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
Consequence
NM_001130823.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNMT1 | NM_001130823.3 | c.687T>G | p.Val229Val | synonymous_variant | Exon 9 of 41 | ENST00000359526.9 | NP_001124295.1 | |
DNMT1 | NM_001318730.2 | c.639T>G | p.Val213Val | synonymous_variant | Exon 8 of 40 | NP_001305659.1 | ||
DNMT1 | NM_001379.4 | c.639T>G | p.Val213Val | synonymous_variant | Exon 8 of 40 | NP_001370.1 | ||
DNMT1 | NM_001318731.2 | c.324T>G | p.Val108Val | synonymous_variant | Exon 9 of 41 | NP_001305660.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152186Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251442Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135908
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727240
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152186Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
DNMT1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Hereditary sensory neuropathy-deafness-dementia syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at