chr10-21538867-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001195626.3(MLLT10):c.195G>A(p.Pro65=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,609,888 control chromosomes in the GnomAD database, including 93,421 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.35 ( 9870 hom., cov: 32)
Exomes 𝑓: 0.33 ( 83551 hom. )
Consequence
MLLT10
NM_001195626.3 synonymous
NM_001195626.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.309
Genes affected
MLLT10 (HGNC:16063): (MLLT10 histone lysine methyltransferase DOT1L cofactor) This gene encodes a transcription factor and has been identified as a partner gene involved in several chromosomal rearrangements resulting in various leukemias. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 10-21538867-G-A is Benign according to our data. Variant chr10-21538867-G-A is described in ClinVar as [Benign]. Clinvar id is 3055784.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-21538867-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.309 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLLT10 | NM_001195626.3 | c.195G>A | p.Pro65= | synonymous_variant | 3/23 | ENST00000307729.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLLT10 | ENST00000307729.12 | c.195G>A | p.Pro65= | synonymous_variant | 3/23 | 1 | NM_001195626.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.350 AC: 53130AN: 151866Hom.: 9850 Cov.: 32
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GnomAD3 exomes AF: 0.306 AC: 76762AN: 250928Hom.: 13239 AF XY: 0.310 AC XY: 42012AN XY: 135638
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GnomAD4 exome AF: 0.331 AC: 482322AN: 1457904Hom.: 83551 Cov.: 31 AF XY: 0.330 AC XY: 239173AN XY: 725412
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GnomAD4 genome ? AF: 0.350 AC: 53201AN: 151984Hom.: 9870 Cov.: 32 AF XY: 0.345 AC XY: 25655AN XY: 74272
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MLLT10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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RBP_binding_hub_radar
RBP_regulation_power_radar
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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