10-21673318-CTTTTTTTTTTTT-CTTTT

Variant names:

• chr10-21673318-CTTTTTTTT-C
• rs397719980
• NM_001195626.3:c.1052-17_1052-10delTTTTTTTT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001195626.3(MLLT10):​c.1052-17_1052-10delTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000394 in 228,516 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: 𝑓 0.000025 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000039 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MLLT10 NM_001195626.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLLT10	NM_001195626.3	c.1052-17_1052-10delTTTTTTTT		intron_variant	Intron 10 of 22	ENST00000307729.12	NP_001182555.1
MLLT10	NM_004641.4	c.1052-17_1052-10delTTTTTTTT		intron_variant	Intron 10 of 23		NP_004632.1
MLLT10	NM_001324297.2	c.317-17_317-10delTTTTTTTT		intron_variant	Intron 12 of 24		NP_001311226.1
MLLT10	NR_136736.2	n.1519-17_1519-10delTTTTTTTT		intron_variant	Intron 11 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLLT10	ENST00000307729.12	c.1052-31_1052-24delTTTTTTTT		intron_variant	Intron 10 of 22	1	NM_001195626.3	ENSP00000307411.7

Frequencies

GnomAD3 genomes AF: 0.0000253 AC: 2 AN: 79132 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000454

Gnomad EAS AF: 0.000404

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000394 AC: 9 AN: 228516 Hom.: 0 AF XY: 0.0000251 AC XY: 3 AN XY: 119348

African (AFR) AF: 0.00 AC: 0 AN: 4912

American (AMR) AF: 0.00 AC: 0 AN: 9670

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4662

East Asian (EAS) AF: 0.00 AC: 0 AN: 11672

South Asian (SAS) AF: 0.0000798 AC: 1 AN: 12538

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13984

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 746

European-Non Finnish (NFE) AF: 0.0000438 AC: 7 AN: 159792

Other (OTH) AF: 0.0000949 AC: 1 AN: 10540

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000253 AC: 2 AN: 79132 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 35944

African (AFR) AF: 0.00 AC: 0 AN: 22074

American (AMR) AF: 0.00 AC: 0 AN: 6352

Ashkenazi Jewish (ASJ) AF: 0.000454 AC: 1 AN: 2204

East Asian (EAS) AF: 0.000404 AC: 1 AN: 2474

South Asian (SAS) AF: 0.00 AC: 0 AN: 1848

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2122

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 150

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 40370

Other (OTH) AF: 0.00 AC: 0 AN: 980

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs397719980; hg19: chr10-21962247;