10-21673318-CTTTTTTTTTTTT-CTTTTTTTTTTT

Variant names:

• chr10-21673318-CT-C
• rs397719980
• NM_001195626.3:c.1052-10delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001195626.3(MLLT10):​c.1052-10delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (1793 hom., cov: 0)
  • Exomes 𝑓: 0.25 (222 hom.)
• Consequence: MLLT10 NM_001195626.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 0 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]

ENSG00000304565 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLLT10	NM_001195626.3	c.1052-10delT		intron_variant	Intron 10 of 22	ENST00000307729.12	NP_001182555.1
MLLT10	NM_004641.4	c.1052-10delT		intron_variant	Intron 10 of 23		NP_004632.1
MLLT10	NM_001324297.2	c.317-10delT		intron_variant	Intron 12 of 24		NP_001311226.1
MLLT10	NR_136736.2	n.1519-10delT		intron_variant	Intron 11 of 25

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.217 AC: 17204 AN: 79194 Hom.: 1789 Cov.: 0

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.259

GnomAD4 exome AF: 0.248 AC: 56451 AN: 227684 Hom.: 222 Cov.: 0 AF XY: 0.244 AC XY: 28954 AN XY: 118898

African (AFR) AF: 0.246 AC: 1208 AN: 4902

American (AMR) AF: 0.157 AC: 1508 AN: 9632

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 1246 AN: 4644

East Asian (EAS) AF: 0.243 AC: 2818 AN: 11590

South Asian (SAS) AF: 0.0975 AC: 1217 AN: 12488

European-Finnish (FIN) AF: 0.175 AC: 2441 AN: 13930

Middle Eastern (MID) AF: 0.275 AC: 205 AN: 746

European-Non Finnish (NFE) AF: 0.271 AC: 43114 AN: 159250

Other (OTH) AF: 0.257 AC: 2694 AN: 10502

GnomAD4 genome AF: 0.217 AC: 17211 AN: 79194 Hom.: 1793 Cov.: 0 AF XY: 0.209 AC XY: 7532 AN XY: 35996

African (AFR) AF: 0.103 AC: 2277 AN: 22092

American (AMR) AF: 0.240 AC: 1534 AN: 6380

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 732 AN: 2206

East Asian (EAS) AF: 0.0377 AC: 93 AN: 2466

South Asian (SAS) AF: 0.173 AC: 319 AN: 1846

European-Finnish (FIN) AF: 0.130 AC: 276 AN: 2120

Middle Eastern (MID) AF: 0.341 AC: 47 AN: 138

European-Non Finnish (NFE) AF: 0.283 AC: 11430 AN: 40400

Other (OTH) AF: 0.264 AC: 260 AN: 986

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs397719980; hg19: chr10-21962247;