21-34859489-GCCCATCCA-G

Variant names:

• chr21-34859489-GCCCATCCA-G
• NM_001754.5:c.590_597delTGGATGGG

Variant summary

Our verdict is Pathogenic. Variant got 2 ACMG points: 2P and 0B. PM5_Supporting PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_001754.5(RUNX1):c.590_597del change is a frameshift variant that is predicted to introduce a premature stop codon and is expected to result in nonsense-mediated mRNA decay. This variant is predicted to affect all the biologically relevant transcripts (PVS1). In addition, this is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting), and it affects AA downstream of c.98 (in transcript NM_001754.4) (PM5_supporting). Although, this has been found in a single patient in a large cohort of AML cases (PMID:27137476), its allele frequency and/or germinal origin is unknown. Therefore, we cannot assess case-study/segregation criteria. In summary, this variant meets the criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PVS1, PM2_supporting, and PM5_supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA2580098634/MONDO:0011071/008

• Frequency: Genomes: not found (cov: 32)
• Consequence: RUNX1 NM_001754.5 frameshift
• Clinical Significance: Pathogenic reviewed by expert panel P:2
• Conservation: PhyloP100: 9.32

Genes affected

RUNX1 (HGNC:10471): (RUNX family transcription factor 1) Core binding factor (CBF) is a heterodimeric transcription factor that binds to the core element of many enhancers and promoters. The protein encoded by this gene represents the alpha subunit of CBF and is thought to be involved in the development of normal hematopoiesis. Chromosomal translocations involving this gene are well-documented and have been associated with several types of leukemia. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000286153 (HGNC:56821): (RUNX1 antisense RNA 1)

ACMG classification

Verdict is Pathogenic. Variant got 2 ACMG points.

• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM5: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RUNX1	NM_001754.5	c.590_597delTGGATGGG	p.Val197AlafsTer13	frameshift_variant	Exon 6 of 9	ENST00000675419.1	NP_001745.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RUNX1	ENST00000675419.1	c.590_597delTGGATGGG	p.Val197AlafsTer13	frameshift_variant	Exon 6 of 9		NM_001754.5	ENSP00000501943.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary thrombocytopenia and hematologic cancer predisposition syndrome Pathogenic:1

Dec 09, 2023

ClinGen Myeloid Malignancy Variant Curation Expert Panel

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The NM_001754.5(RUNX1):c.590_597del change is a frameshift variant that is predicted to introduce a premature stop codon and is expected to result in nonsense-mediated mRNA decay. This variant is predicted to affect all the biologically relevant transcripts (PVS1). In addition, this is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting), and it affects AA downstream of c.98 (in transcript NM_001754.4) (PM5_supporting). Although, this has been found in a single patient in a large cohort of AML cases (PMID: 27137476), its allele frequency and/or germinal origin is unknown. Therefore, we cannot assess case-study/segregation criteria. In summary, this variant meets the criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PVS1, PM2_supporting, and PM5_supporting. -

Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Pathogenic:1

Sep 22, 2022

Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr21-36231786;