10-21532345-G-A

Variant names:

• chr10-21532345-G-A
• rs7084454
• ENST00000631589.1:c.1-2300G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000631589.1(MLLT10):​c.1-2300G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,948 control chromosomes in the GnomAD database, including 8,481 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 0.32 (8481 hom., cov: 32)
• Consequence: MLLT10 ENST00000631589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.601
• Publications: 32 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLLT10	ENST00000631589.1	c.1-2300G>A		intron_variant	Intron 1 of 22	5		ENSP00000488569.1
MLLT10	ENST00000651097.1	c.-197-6488G>A		intron_variant	Intron 1 of 5			ENSP00000498343.1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49191 AN: 151828 Hom.: 8458 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.0140

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.370

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.324 AC: 49263 AN: 151948 Hom.: 8481 Cov.: 32 AF XY: 0.319 AC XY: 23678 AN XY: 74256

African (AFR) AF: 0.376 AC: 15605 AN: 41462

American (AMR) AF: 0.275 AC: 4194 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3468

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5192

South Asian (SAS) AF: 0.198 AC: 954 AN: 4824

European-Finnish (FIN) AF: 0.314 AC: 3313 AN: 10536

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22390 AN: 67884

Other (OTH) AF: 0.374 AC: 787 AN: 2106

Alfa AF: 0.325 Hom.: 2379

Bravo AF: 0.325

Asia WGS AF: 0.167 AC: 580 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	15
DANN	Benign	0.58
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs7084454; hg19: chr10-21821274;