rs1243182

chr10-21627799-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195626.3(MLLT10):c.699+10592C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,854 control chromosomes in the GnomAD database, including 11,191 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 0.37 (11191 hom., cov: 32)
• Consequence: MLLT10 NM_001195626.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLLT10	NM_001195626.3	c.699+10592C>T		intron_variant		ENST00000307729.12
MLLT10	NM_001324297.2	c.-173+10592C>T		intron_variant
MLLT10	NM_004641.4	c.699+10592C>T		intron_variant
MLLT10	NR_136736.2	n.1166+10592C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLLT10	ENST00000307729.12	c.699+10592C>T		intron_variant		1	NM_001195626.3	P1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55754 AN: 151736 Hom.: 11153 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.368 AC: 55855 AN: 151854 Hom.: 11191 Cov.: 32 AF XY: 0.364 AC XY: 27043 AN XY: 74210

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.412

Alfa AF: 0.335 Hom.: 12555

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.98
Dann	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1243182; hg19: chr10-21916728;