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]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_001754.5(RUNX1):c.1007T>C (p.Phe336Ser)

CA10014221

409815 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: e2605f35-9cc0-43b3-a55f-9c0cb9ca43ce
Approved on: 2024-09-30
Published on: 2024-09-30

HGVS expressions

NM_001754.5:c.1007T>C
NM_001754.5(RUNX1):c.1007T>C (p.Phe336Ser)
NC_000021.9:g.34792571A>G
CM000683.2:g.34792571A>G
NC_000021.8:g.36164868A>G
CM000683.1:g.36164868A>G
NC_000021.7:g.35086738A>G
NG_011402.2:g.1197141T>C
ENST00000675419.1:c.1007T>C
ENST00000300305.7:c.1007T>C
ENST00000344691.8:c.926T>C
ENST00000399240.5:c.734T>C
ENST00000437180.5:c.1007T>C
ENST00000482318.5:c.*597T>C
NM_001001890.2:c.926T>C
NM_001754.4:c.1007T>C
NM_001001890.3:c.926T>C
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Uncertain Significance

Met criteria codes 2
BS1 PP3
Not Met criteria codes 24
PVS1 BA1 PM6 PM2 PM3 PM1 PM4 PM5 BS4 BS3 BS2 BP2 BP3 BP4 BP1 BP5 BP7 PS4 PS2 PS3 PS1 PP4 PP1 PP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Myeloid Malignancy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
NM_001754.4:c.1007T>C is a missense variant which has an MAF of 0.0002133 (0.02%, 7/32818 alleles) in the Latino subpopulation of the gnomAD v2.1.1 cohort, which is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). This missense variant has a REVEL score >0.75 (0.791) (PP3). The variant has not been reported in the germ line of patients with familial platelet disorder with predisposition to hematologic malignancies in the literature, to the best of our knowledge. 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: BS1, PP3.
Met criteria codes
BS1
The variant is reported at a frequency of 0.0002133 (7/32818 Latino alleles) in gnomAD v.2.1.1. It is absent from gnomAD v3. The variant meets criteria for BS1 based on the gnomAD v2 frequency; threshold: >0.00015
PP3
The variant has a REVEL score of 0.791, which meets criteria for PP3 (threshold: >0.75)
Not Met criteria codes
PVS1
N/A
BA1
Meets BS1
PM6
No data currently available
PM2
Meets BS1
PM3
MM-VCEP deemed N/A for RUNX1
PM1
N/A
PM4
N/A
PM5
No data currently available
BS4
No data currently available
BS3
No data currently available
BS2
MM-VCEP deemed N/A for RUNX1
BP2
N/A
BP3
MM-VCEP deemed N/A for RUNX1
BP4
Meets PP3
BP1
MM-VCEP deemed N/A for RUNX1
BP5
MM-VCEP deemed N/A for RUNX1
BP7
N/A
PS4
The variant has not been reported in the germ line of patients with familial platelet disorder with predisposition to hematologic malignancies in the literature, to the best of our knowledge.
PS2
No data currently available
PS3
No data currently available
PS1
No data currently available
PP4
MM-VCEP deemed N/A for RUNX1
PP1
No data currently available
PP2
MM-VCEP deemed N/A for RUNX1
Curation History
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