NM_001754.5(RUNX1):c.339del (p.Ile114fs) AND Hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 5, 2022
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002264724.1

Allele description [Variation Report for NM_001754.5(RUNX1):c.339del (p.Ile114fs)]

NM_001754.5(RUNX1):c.339del (p.Ile114fs)

Gene:

RUNX1:RUNX family transcription factor 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

21q22.12

Genomic location:

Preferred name:

NM_001754.5(RUNX1):c.339del (p.Ile114fs)

Other names:

NM_001754.5(RUNX1):c.339del; p.Ile114fs

HGVS:

NC_000021.9:g.34886857del
NG_011402.2:g.1102857del
NM_001001890.3:c.258del
NM_001122607.2:c.258del
NM_001754.5:c.339delMANE SELECT
NP_001001890.1:p.Ile87fs
NP_001116079.1:p.Ile87fs
NP_001745.2:p.Ile114fs
LRG_482:g.1102857del
NC_000021.8:g.36259154del
NM_001754.4:c.339delC

Protein change:

I114fs

Links:

dbSNP: rs1569084032

NCBI 1000 Genomes Browser:

rs1569084032

Molecular consequence:

NM_001001890.3:c.258del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001122607.2:c.258del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001754.5:c.339del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Identifiers:: MONDO: MONDO:0011071; MedGen: CN281654

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002546428	ClinGen Myeloid Malignancy Variant Curation Expert Panel	reviewed by expert panel (ClinGen MyeloMalig ACMG Specifications v2)	Likely pathogenic (Jul 5, 2022)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002546428

ClinGen Myeloid Malignancy Variant Curation Expert Panel

reviewed by expert panel

(ClinGen MyeloMalig ACMG Specifications v2)

Likely pathogenic
(Jul 5, 2022)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Details of each submission

From ClinGen Myeloid Malignancy Variant Curation Expert Panel, SCV002546428.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

NM_001754.5(RUNX1):c.339del (p.Ile114fs) is a frameshift variant predicted to undergo NMD (PVS1 SNV tree). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting).In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PVS1 and PM2_supporting

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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