Variant 1-151067437-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_006818.4(MLLT11):c.213C>T(p.Thr71=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00474 in 1,614,138 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0049 ( 29 hom. )

Consequence

MLLT11
NM_006818.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.74

Variant links:

Genes affected

MLLT11 (HGNC:16997): (MLLT11 transcription factor 7 cofactor) The gene variously symbolized ALL1, HRX, or MLL located on 11q23 has been demonstrated to be fused with a number of translocation partners in cases of leukemia. t(1;11)(q21;q23) translocations that fused the MLL gene to a gene on chromosomal band 1q21 in 2 infants with acute myelomonocytic leukemia have been demonstrated. The N-terminal portion of the MLL gene is critical for leukemogenesis in translocations involving band 11q23. This gene encodes 90 amino acids. It was found to be highly expressed in the thymus but not in peripheral lymphoid tissues. In contrast to its restricted distribution in normal hematopoietic tissue, this gene was expressed in all leukemic cell lines tested. [provided by RefSeq, Jul 2008]

MLLT11 links:

CDC42SE1 (HGNC:17719): (CDC42 small effector 1) Predicted to enable GTPase inhibitor activity. Predicted to be involved in signal transduction. Located in cell junction. [provided by Alliance of Genome Resources, Apr 2022]

CDC42SE1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BP6

Variant 1-151067437-C-T is Benign according to our data. Variant chr1-151067437-C-T is described in ClinVar as [Benign]. Clinvar id is 708650.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.74 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLLT11	NM_006818.4 linkuse as main transcript	c.213C>T	p.Thr71=	synonymous_variant	2/2	ENST00000368921.5	NP_006809.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLLT11	ENST00000368921.5 linkuse as main transcript	c.213C>T	p.Thr71=	synonymous_variant	2/2	1	NM_006818.4	ENSP00000357917	P1
CDC42SE1	ENST00000439374.6 linkuse as main transcript	c.-761-103G>A		intron_variant		5		ENSP00000475845	P1	Q9NRR8-1

Frequencies

GnomAD3 genomes

AF:

0.00324

AC:

493

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000773

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00807

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00489

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00394

AC:

990

AN:

251470

Hom.:

AF XY:

0.00443

AC XY:

602

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.000677

Gnomad AMR exome

AF:

0.00205

Gnomad ASJ exome

AF:

0.00367

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00790

Gnomad FIN exome

AF:

0.000277

Gnomad NFE exome

AF:

0.00531

Gnomad OTH exome

AF:

0.00310

GnomAD4 exome

AF:

0.00489

AC:

7152

AN:

1461886

Hom.:

Cov.:

AF XY:

0.00500

AC XY:

3636

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.000687

Gnomad4 AMR exome

AF:

0.00192

Gnomad4 ASJ exome

AF:

0.00386

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00754

Gnomad4 FIN exome

AF:

0.000505

Gnomad4 NFE exome

AF:

0.00533

Gnomad4 OTH exome

AF:

0.00459

GnomAD4 genome

AF:

0.00324

AC:

494

AN:

152252

Hom.:

Cov.:

AF XY:

0.00304

AC XY:

226

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.000771

Gnomad4 AMR

AF:

0.00367

Gnomad4 ASJ

AF:

0.00518

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00829

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00489

Gnomad4 OTH

AF:

0.00425

Alfa

AF:

0.00464

Hom.:

Bravo

AF:

0.00332

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00556

EpiControl

AF:

0.00492

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 04, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.77

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over