chr19-10149567-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001130823.3(DNMT1):c.2472G>A(p.Thr824Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000667 in 1,613,976 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNMT1 | NM_001130823.3 | c.2472G>A | p.Thr824Thr | synonymous_variant | Exon 26 of 41 | ENST00000359526.9 | NP_001124295.1 | |
DNMT1 | NM_001318730.2 | c.2424G>A | p.Thr808Thr | synonymous_variant | Exon 25 of 40 | NP_001305659.1 | ||
DNMT1 | NM_001379.4 | c.2424G>A | p.Thr808Thr | synonymous_variant | Exon 25 of 40 | NP_001370.1 | ||
DNMT1 | NM_001318731.2 | c.2109G>A | p.Thr703Thr | synonymous_variant | Exon 26 of 41 | NP_001305660.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000619 AC: 94AN: 151970Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000402 AC: 101AN: 251226Hom.: 0 AF XY: 0.000457 AC XY: 62AN XY: 135782
GnomAD4 exome AF: 0.000672 AC: 983AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.000634 AC XY: 461AN XY: 727242
GnomAD4 genome AF: 0.000618 AC: 94AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.000525 AC XY: 39AN XY: 74332
ClinVar
Submissions by phenotype
not provided Benign:3
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DNMT1: BP4, BP7 -
Hereditary sensory neuropathy-deafness-dementia syndrome Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at