Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001754.5(RUNX1):c.899C>T (p.Thr300Met)

CA10014273

409809 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: b0d433bc-d13c-413f-877d-554f4902abb1
Approved on: 2023-11-13
Published on: 2023-11-13

HGVS expressions

NM_001754.5:c.899C>T
NM_001754.5(RUNX1):c.899C>T (p.Thr300Met)
NC_000021.9:g.34799369G>A
CM000683.2:g.34799369G>A
NC_000021.8:g.36171666G>A
CM000683.1:g.36171666G>A
NC_000021.7:g.35093536G>A
NG_011402.2:g.1190343C>T
ENST00000675419.1:c.899C>T
ENST00000300305.7:c.899C>T
ENST00000344691.8:c.818C>T
ENST00000399240.5:c.626C>T
ENST00000437180.5:c.899C>T
ENST00000482318.5:c.*489C>T
NM_001001890.2:c.818C>T
NM_001754.4:c.899C>T
NM_001001890.3:c.818C>T
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Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 25
BS2 BS4 BS3 BS1 BP2 BP3 BP1 BP7 BP5 PS4 PS2 PS1 PS3 BA1 PP4 PP1 PP3 PP2 PM5 PM1 PM3 PM4 PM6 PM2 PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
NM_001754.5(RUNX1):c.899C>T (p.Thr300Met) is a missense variant. This variant has been seen in gnomADv2.1 at a MAF of 0.00005274 (0.005274%, 6/113766 in the European(non-Finnish) sub-population). This variant does not meet any population criteria. This missense variant has a REVEL score <0.50 (0.423)(BP4). There is no splicing effect predicted (SpliceAI=0). The variant has not been reported in patients with the RUNX1-defined phenotype. In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4
Met criteria codes
BP4
This missense variant has a REVEL score <0.50 (0.423).
Not Met criteria codes
BS2
This rule is not applicable for MM-VCEP
BS4
No case study found
BS3
No functional studies found
BS1
This variant has been seen in gnomADv2.1 at a MAF of 0.00005274 (0.005274%, 6/113766 in the European(non-Finnish) sub-population). This variant does not meet any population criteria.
BP2
No case study found
BP3
This rule is not applicable for MM-VCEP
BP1
This rule is not applicable for MM-VCEP
BP7
Missense variant
BP5
This rule is not applicable for MM-VCEP
PS4
No case study found
PS2
No case study found
PS1
No pathogenic variant has been identified at this amino acid (a.a. 300)
PS3
No functional studies found
BA1
This variant has been seen in gnomADv2.1 at a MAF of 0.00005274 (0.005274%, 6/113766 in the European(non-Finnish) sub-population). This variant does not meet any population criteria.
PP4
This rule is not applicable for MM-VCEP
PP1
No case study found
PP3
BP4 Met
PP2
This rule is not applicable for MM-VCEP
PM5
No pathogenic variant has been identified at this amino acid (a.a. 300)
PM1
This variant does not affect one of the hotspot residues established by the MM-VCEP for RUNX1
PM3
This rule is not applicable for MM-VCEP
PM4
Missense variant
PM6
No case study found
PM2
This variant has been seen in gnomADv2.1 at a MAF of 0.00005274 (0.005274%, 6/113766 in the European(non-Finnish) sub-population). This variant does not meet any population criteria.
PVS1
Missense variant
Curation History
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