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NM_001754.5(RUNX1):c.291C>T (p.Phe97=) AND Hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Nov 13, 2023
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:
RCV003405645.1

Allele description [Variation Report for NM_001754.5(RUNX1):c.291C>T (p.Phe97=)]

NM_001754.5(RUNX1):c.291C>T (p.Phe97=)

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.291C>T (p.Phe97=)
Other names:
NM_001754.5(RUNX1):c.291C>T; p.Phe97=
HGVS:
  • NC_000021.9:g.34886903G>A
  • NG_011402.2:g.1102809C>T
  • NM_001001890.3:c.210C>T
  • NM_001122607.2:c.210C>T
  • NM_001754.5:c.291C>TMANE SELECT
  • NP_001001890.1:p.Phe70=
  • NP_001116079.1:p.Phe70=
  • NP_001745.2:p.Phe97=
  • LRG_482:g.1102809C>T
  • NC_000021.8:g.36259200G>A
Links:
dbSNP: rs1432236291
NCBI 1000 Genomes Browser:
rs1432236291
Molecular consequence:
  • NM_001001890.3:c.210C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001122607.2:c.210C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001754.5:c.291C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

Recent activity

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  • Homo sapiens NHS like 3 (NHSL3), transcript variant 4, mRNA
    Homo sapiens NHS like 3 (NHSL3), transcript variant 4, mRNA
    gi|1613450168|ref|NM_001369553.1|
    Nucleotide
  • JC Virus
    JC Virus
    A species of POLYOMAVIRUS, originally isolated from the brain of a patient with progressive multifocal leukoencephalopathy. The patient's initials J.C. gave the virus its name...<br/>Year introduced: 2002, 1983-1993
    MeSH

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004123196ClinGen Myeloid Malignancy Variant Curation Expert Panel
reviewed by expert panel

(ClinGen MyeloMalig ACMG Specifications v2)		Likely benign
(Nov 13, 2023) 		germlinecuration

Citation Link

Help

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, SCV004123196.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The NM_001754.5(RUNX1):c.291C>T (p.Phe97=) variant is reported at a MAF of 0.00005 (0.005%, 1/21626 alleles) in the non-Finnish European subpopulation of the gnomAD v2.1.1 cohort, and does not meet thresholds for BA1, BS1, or PM2. The variant has not been reported in patients with familial platelet disorder with predisposition to hematologic malignancies in the literature, to the best of our knowledge. REVEL score is not calculable for a synonymous variant; SpiceAI predicts: Acceptor loss 0.02, Donor loss 0.00, Acceptor gain 0.00, Donor gain 0.00. Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 0.74248< 2.0) In summary, the clinical significance of this variant is likely benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7.

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

Last Updated: Sep 29, 2024