chr2-25248091-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_022552.5(DNMT3A):c.801C>T(p.Ser267Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00268 in 1,613,112 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_022552.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00240 AC: 365AN: 152138Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00249 AC: 620AN: 248854Hom.: 2 AF XY: 0.00239 AC XY: 322AN XY: 134714
GnomAD4 exome AF: 0.00271 AC: 3954AN: 1460858Hom.: 11 Cov.: 32 AF XY: 0.00257 AC XY: 1866AN XY: 726664
GnomAD4 genome AF: 0.00240 AC: 366AN: 152254Hom.: 1 Cov.: 32 AF XY: 0.00234 AC XY: 174AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:5
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DNMT3A: BP4, BP7 -
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Tatton-Brown-Rahman overgrowth syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at