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NM_001754.5(RUNX1):c.351+2T>A AND Hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 24, 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:
RCV002264769.1

Allele description [Variation Report for NM_001754.5(RUNX1):c.351+2T>A]

NM_001754.5(RUNX1):c.351+2T>A

Gene:
RUNX1:RUNX family transcription factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.12
Genomic location:
Preferred name:
NM_001754.5(RUNX1):c.351+2T>A
HGVS:
  • NC_000021.9:g.34886841A>T
  • NG_011402.2:g.1102871T>A
  • NG_144242.1:g.316A>T
  • NM_001001890.3:c.270+2T>A
  • NM_001122607.2:c.270+2T>A
  • NM_001754.5:c.351+2T>AMANE SELECT
  • LRG_482t1:c.351+2T>A
  • LRG_482:g.1102871T>A
  • NC_000021.8:g.36259138A>T
  • NM_001754.4:c.351+2T>A
Links:
dbSNP: rs2057997150
NCBI 1000 Genomes Browser:
rs2057997150
Molecular consequence:
  • NM_001001890.3:c.270+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001122607.2:c.270+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001754.5:c.351+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002546442ClinGen Myeloid Malignancy Variant Curation Expert Panel
reviewed by expert panel

(ClinGen MyeloMalig ACMG Specifications v2)		Likely pathogenic
(Apr 24, 2022) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Myeloid Malignancy Variant Curation Expert Panel, SCV002546442.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.351+2T>A is a splice donor variant that is predicted to introduce exon 4 skipping and a frameshift with a premature stop codon and is expected to result in nonsense-mediated mRNA decay (PVS1). 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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024