rs1243180

chr10-21626690-T-Achr10-21626690-T-G

Variant summary

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

The NM_001195626.3(MLLT10):c.699+9483T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,130 control chromosomes in the GnomAD database, including 5,168 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 0.23 (5168 hom., cov: 32)
• Consequence: MLLT10 NM_001195626.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLLT10	NM_001195626.3	c.699+9483T>A		intron_variant		ENST00000307729.12
MLLT10	NM_001324297.2	c.-173+9483T>A		intron_variant
MLLT10	NM_004641.4	c.699+9483T>A		intron_variant
MLLT10	NR_136736.2	n.1166+9483T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLLT10	ENST00000307729.12	c.699+9483T>A		intron_variant		1	NM_001195626.3	P1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35255 AN: 152012 Hom.: 5159 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.232 AC: 35268 AN: 152130 Hom.: 5168 Cov.: 32 AF XY: 0.233 AC XY: 17350 AN XY: 74364

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.292

Alfa AF: 0.157 Hom.: 336

Bravo AF: 0.225

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.0
Dann	Benign	0.82

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: rs1243180; hg19: chr10-21915619;