Genetic Variant NM_001195626.3:c.1052-16_1052-10delTTTTTTT (chr10-21673318-CTTTTTTT-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001195626.3(MLLT10):c.1052-16_1052-10delTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000325 in 307,642 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000051 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000026 ( 0 hom. )

Consequence

MLLT10
NM_001195626.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.414

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: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MLLT10	NM_001195626.3 link	c.1052-16_1052-10delTTTTTTT	intron_variant	Intron 10 of 22	ENST00000307729.12	NP_001182555.1	P55197-4Q59EQ6Q6N002
MLLT10	NM_004641.4 link	c.1052-16_1052-10delTTTTTTT	intron_variant	Intron 10 of 23		NP_004632.1	P55197-1Q59EQ6Q6N002
MLLT10	NM_001324297.2 link	c.317-16_317-10delTTTTTTT	intron_variant	Intron 12 of 24		NP_001311226.1
MLLT10	NR_136736.2 link	n.1519-16_1519-10delTTTTTTT	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_1052-25delTTTTTTT		intron_variant	Intron 10 of 22	1	NM_001195626.3	ENSP00000307411.7		P55197-4

Frequencies

GnomAD3 genomes

AF:

0.0000505

AC:

AN:

79132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000453

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000808

Gnomad SAS

AF:

0.000541

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000263

AC:

AN:

228510

Hom.:

AF XY:

0.0000251

AC XY:

AN XY:

119342

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:

0.0000857

AC:

AN:

11670

South Asian (SAS)

AF:

0.00

AC:

AN:

12536

European-Finnish (FIN)

AF:

0.00

AC:

AN:

13984

Middle Eastern (MID)

AF:

0.00

AC:

AN:

746

European-Non Finnish (NFE)

AF:

0.0000250

AC:

AN:

159790

Other (OTH)

AF:

0.0000949

AC:

AN:

10540

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000505

AC:

AN:

79132

Hom.:

Cov.:

AF XY:

0.0000278

AC XY:

AN XY:

35960

show subpopulations

African (AFR)

AF:

0.0000453

AC:

AN:

22086

American (AMR)

AF:

0.00

AC:

AN:

6360

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2204

East Asian (EAS)

AF:

0.000811

AC:

AN:

2466

South Asian (SAS)

AF:

0.000542

AC:

AN:

1846

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2122

Middle Eastern (MID)

AF:

0.00

AC:

AN:

138

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

40366

Other (OTH)

AF:

0.00

AC:

AN:

986

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

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.41

Splicing

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

Publications

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NM_001195626.3:c.1052-16_1052-10delTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over