Genetic Variant MLLT10:c.1052-21_1052-10delTTTTTTTTTTTT (chr10-21673318-CTTTTTTTTTTTT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001195626.3(MLLT10):c.1052-21_1052-10delTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000438 in 228,518 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.0000044 ( 0 hom. )

Consequence

MLLT10
NM_001195626.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.707

Publications

0 publications found

Variant links:

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]

MLLT10 links:

ENSG00000304565 (HGNC:):

ENSG00000304565 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MLLT10	NM_001195626.3 link	c.1052-21_1052-10delTTTTTTTTTTTT	intron_variant	Intron 10 of 22	ENST00000307729.12	NP_001182555.1	P55197-4Q59EQ6Q6N002
MLLT10	NM_004641.4 link	c.1052-21_1052-10delTTTTTTTTTTTT	intron_variant	Intron 10 of 23		NP_004632.1	P55197-1Q59EQ6Q6N002
MLLT10	NM_001324297.2 link	c.317-21_317-10delTTTTTTTTTTTT	intron_variant	Intron 12 of 24		NP_001311226.1
MLLT10	NR_136736.2 link	n.1519-21_1519-10delTTTTTTTTTTTT	intron_variant	Intron 11 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLLT10	ENST00000307729.12 link	c.1052-31_1052-20delTTTTTTTTTTTT		intron_variant	Intron 10 of 22	1	NM_001195626.3	ENSP00000307411.7		P55197-4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000438

AC:

AN:

228518

Hom.:

AF XY:

0.00000838

AC XY:

AN XY:

119350

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

4912

American (AMR)

AF:

0.00

AC:

AN:

9670

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4662

East Asian (EAS)

AF:

0.00

AC:

AN:

11672

South Asian (SAS)

AF:

0.00

AC:

AN:

12538

European-Finnish (FIN)

AF:

0.0000715

AC:

AN:

13984

Middle Eastern (MID)

AF:

0.00

AC:

AN:

746

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

159794

Other (OTH)

AF:

0.00

AC:

AN:

10540

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over