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NM_001754.5(RUNX1):c.58+264C>T AND Hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Germline classification:
Benign (1 submission)
Last evaluated:
Sep 10, 2024
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:
RCV004699439.1

Allele description [Variation Report for NM_001754.5(RUNX1):c.58+264C>T]

NM_001754.5(RUNX1):c.58+264C>T

Genes:
LOC130066606:ATAC-STARR-seq lymphoblastoid active region 18416 [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.58+264C>T
HGVS:
  • NC_000021.9:g.35048578G>A
  • NG_011402.2:g.941134C>T
  • NM_001754.5:c.58+264C>TMANE SELECT
  • LRG_482:g.941134C>T
  • NC_000021.8:g.36420875G>A
Links:
dbSNP: rs9981811
NCBI 1000 Genomes Browser:
rs9981811
Molecular consequence:
  • NM_001754.5:c.58+264C>T - intron variant - [Sequence Ontology: SO:0001627]

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
SCV005205698ClinGen Myeloid Malignancy Variant Curation Expert Panel
reviewed by expert panel

(ClinGen MyeloMalig ACMG Specifications v2)		Benign
(Sep 10, 2024) 		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, SCV005205698.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_001754.5(RUNX1):c.58+264C>T is an intronic variant with a MAF of 0.08337(8.337%, 1286/15426,) in the European subpopulation of gnomAD cohort is ≥ 0.0015 (0.15%) (BA1). This variant is observed in 70 homozygotes in a population database (gnomAD) (BP2). This variant has a SpliceAI score ≤ 0.20 (Donor Loss 0.05) (BP4). Evolutionary conservation algorithms predict the site as not being conserved (PhyloP score -1.17 < 2.0 or the variant is the reference nucleotide in one primate (Rhesus) (BP7). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4, BP7.

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

Last Updated: Sep 29, 2024