rs2864419
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032482.3(DOT1L):c.125+2420G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,928 control chromosomes in the GnomAD database, including 15,382 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.45 ( 15382 hom., cov: 31)
Consequence
DOT1L
NM_032482.3 intron
NM_032482.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.407
Genes affected
DOT1L (HGNC:24948): (DOT1 like histone lysine methyltransferase) The protein encoded by this gene is a histone methyltransferase that methylates lysine-79 of histone H3. It is inactive against free core histones, but shows significant histone methyltransferase activity against nucleosomes. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOT1L | NM_032482.3 | c.125+2420G>T | intron_variant | ENST00000398665.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOT1L | ENST00000398665.8 | c.125+2420G>T | intron_variant | 1 | NM_032482.3 | P2 | |||
DOT1L | ENST00000452696.5 | c.125+2420G>T | intron_variant | 3 | |||||
DOT1L | ENST00000686010.1 | c.125+2420G>T | intron_variant | A2 | |||||
DOT1L | ENST00000478937.3 | c.112+2420G>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.448 AC: 68081AN: 151810Hom.: 15370 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.448 AC: 68122AN: 151928Hom.: 15382 Cov.: 31 AF XY: 0.448 AC XY: 33305AN XY: 74272
GnomAD4 genome
?
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68122
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31
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33305
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74272
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1499
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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