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NM_001754.5(RUNX1):c.393T>C (p.Thr131=) AND Hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jun 22, 2021
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:
RCV003411840.1

Allele description [Variation Report for NM_001754.5(RUNX1):c.393T>C (p.Thr131=)]

NM_001754.5(RUNX1):c.393T>C (p.Thr131=)

Genes:
RUNX1:RUNX family transcription factor 1 [Gene - OMIM - HGNC]
RUNX1-AS1:RUNX1 antisense RNA 1 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.12
Genomic location:
Preferred name:
NM_001754.5(RUNX1):c.393T>C (p.Thr131=)
Other names:
NM_001754.4(RUNX1):c.393T>C; p.Thr131=
HGVS:
  • NC_000021.9:g.34880672A>G
  • NG_011402.2:g.1109040T>C
  • NM_001001890.3:c.312T>C
  • NM_001122607.2:c.312T>C
  • NM_001754.5:c.393T>CMANE SELECT
  • NP_001001890.1:p.Thr104=
  • NP_001116079.1:p.Thr104=
  • NP_001745.2:p.Thr131=
  • NP_001745.2:p.Thr131=
  • LRG_482t1:c.393T>C
  • LRG_482:g.1109040T>C
  • LRG_482p1:p.Thr131=
  • NC_000021.8:g.36252969A>G
  • NM_001754.4:c.393T>C
Links:
dbSNP: rs746650216
NCBI 1000 Genomes Browser:
rs746650216
Molecular consequence:
  • NM_001001890.3:c.312T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001122607.2:c.312T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001754.5:c.393T>C - 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
SCV004123282ClinGen Myeloid Malignancy Variant Curation Expert Panel
reviewed by expert panel

(ClinGen MyeloMalig ACMG Specifications v2)		Likely benign
(Jun 22, 2021) 		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, SCV004123282.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.393T>C predicts a synonymous change, Thr131= variant and has an MAF of 0.001013 (0.1%, 31/30616 alleles) in the African subpopulation of the gnomAD v2.1.1 cohort and is >= 0.00015 (0.015%) (BS1). This variant is detected in a homozygous state in 1 individual in the gnomAD v2.1.1 population database (BP2). This synonymous variant is predicted by SSF and MES to lead to either an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% and no putative cryptic splice sites are created (BP4). In addition, evolutionary conservation prediction algorithms predict the site as not being highly conserved (PhyloP score -4.47871 < 0.1) (BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BS1, BP2, BP4, BP7.

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

Last Updated: Sep 29, 2024