chr10-21612326-CTT-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001195626.3(MLLT10):c.406-11_406-10del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0063 in 1,194,506 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0071 ( 0 hom. )
Consequence
MLLT10
NM_001195626.3 intron
NM_001195626.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.05
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 10-21612326-CTT-C is Benign according to our data. Variant chr10-21612326-CTT-C is described in ClinVar as [Benign]. Clinvar id is 3050487.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 28 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLLT10 | NM_001195626.3 | c.406-11_406-10del | intron_variant | ENST00000307729.12 | |||
MLLT10 | NM_001324297.2 | c.-466-11_-466-10del | intron_variant | ||||
MLLT10 | NM_004641.4 | c.406-11_406-10del | intron_variant | ||||
MLLT10 | NR_136736.2 | n.873-11_873-10del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLLT10 | ENST00000307729.12 | c.406-11_406-10del | intron_variant | 1 | NM_001195626.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000195 AC: 28AN: 143226Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.00714 AC: 7502AN: 1051280Hom.: 0 AF XY: 0.00735 AC XY: 3885AN XY: 528306
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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 | Jul 15, 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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at