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NM_001754.5(RUNX1):c.300C>G (p.Ser100=) AND Hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 7, 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:
RCV002264709.1

Allele description [Variation Report for NM_001754.5(RUNX1):c.300C>G (p.Ser100=)]

NM_001754.5(RUNX1):c.300C>G (p.Ser100=)

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.300C>G (p.Ser100=)
Other names:
NM_001754.5(RUNX1):c.300C>G; p.Ser100=
HGVS:
  • NC_000021.9:g.34886894G>C
  • NG_011402.2:g.1102818C>G
  • NM_001001890.3:c.219C>G
  • NM_001122607.2:c.219C>G
  • NM_001754.5:c.300C>GMANE SELECT
  • NP_001001890.1:p.Ser73=
  • NP_001116079.1:p.Ser73=
  • NP_001745.2:p.Ser100=
  • NP_001745.2:p.Ser100=
  • LRG_482t1:c.300C>G
  • LRG_482:g.1102818C>G
  • LRG_482p1:p.Ser100=
  • NC_000021.8:g.36259191G>C
  • NM_001754.4:c.300C>G
Links:
dbSNP: rs764387069
NCBI 1000 Genomes Browser:
rs764387069
Molecular consequence:
  • NM_001001890.3:c.219C>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001122607.2:c.219C>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001754.5:c.300C>G - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV002546371ClinGen Myeloid Malignancy Variant Curation Expert Panel
reviewed by expert panel

(ClinGen MyeloMalig ACMG Specifications v2)		Likely benign
(Jul 7, 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, SCV002546371.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_001754.5(RUNX1):c.300C>G (p.Ser100=) is a synonymous variant. In summary, this variant meets the criteria to be classified as likely benign. Therefore, a REVEL score is not calculable. SpliceAI prediction suggests Acceptor loss 0, Donor loss 0, Acceptor gain 0, Donor gain 0. Therefore, there appears to be no effect on splicing (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.302402 < 2.0)(BP7 ). This variant is completely absent from all population databases with at least 20x coverage for RUNX1(PM2_supporting). ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7, PM2_supporting.

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

Last Updated: Sep 29, 2024