rs369797804

Variant names:

• chr10-21612326-CTTTTT-C
• rs369797804
• NM_001195626.3:c.406-14_406-10delTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr10-21612326-CTTTTT-C
• chr10-21612326-CTTTTT-CT
• chr10-21612326-CTTTTT-CTT
• chr10-21612326-CTTTTT-CTTT
• chr10-21612326-CTTTTT-CTTTT
• chr10-21612326-CTTTTT-CTTTTTT
• chr10-21612326-CTTTTT-CTTTTTTT
• chr10-21612326-CTTTTT-CTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001195626.3(MLLT10):​c.406-14_406-10delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000091 in 1,098,986 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: not found (cov: 30)
  • Exomes 𝑓: 9.1e-7 (0 hom.)
• Consequence: MLLT10 NM_001195626.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.05
• 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195626.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLLT10	NM_001195626.3	MANE Select	c.406-14_406-10delTTTTT		intron	N/A	NP_001182555.1	P55197-4
	MLLT10	NM_004641.4		c.406-14_406-10delTTTTT		intron	N/A	NP_004632.1	P55197-1
	MLLT10	NM_001324297.2		c.-466-14_-466-10delTTTTT		intron	N/A	NP_001311226.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLLT10	ENST00000307729.12	TSL:1 MANE Select	c.406-14_406-10delTTTTT		intron	N/A	ENSP00000307411.7	P55197-4
	MLLT10	ENST00000377059.7	TSL:1	c.406-14_406-10delTTTTT		intron	N/A	ENSP00000366258.4	P55197-4
	MLLT10	ENST00000377072.8	TSL:1	c.406-14_406-10delTTTTT		intron	N/A	ENSP00000366272.3	P55197-1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 9.10e-7 AC: 1 AN: 1098986 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 552700

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 24880

American (AMR) AF: 0.00 AC: 0 AN: 29820

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20892

East Asian (EAS) AF: 0.00 AC: 0 AN: 34134

South Asian (SAS) AF: 0.00 AC: 0 AN: 66740

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40936

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4528

European-Non Finnish (NFE) AF: 0.00000120 AC: 1 AN: 830690

Other (OTH) AF: 0.00 AC: 0 AN: 46366

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs369797804; hg19: chr10-21901255;