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.781C>T (p.Pro261Ser)

CA410206700

1515908 (ClinVar)

Gene: RUNX1 (HGNC:861)
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome (MONDO:0011071)
Inheritance Mode: Autosomal dominant inheritance
UUID: 55b2ea7f-2880-4508-8f5f-f5af9204e0fc
Approved on: 2025-01-15
Published on: 2025-01-15

HGVS expressions

NM_001754.5(RUNX1):c.781C>T (p.Pro261Ser)
NM_001754.5:c.781C>T
NC_000021.9:g.34834434G>A
CM000683.2:g.34834434G>A
NC_000021.8:g.36206731G>A
CM000683.1:g.36206731G>A
NC_000021.7:g.35128601G>A
NG_011402.2:g.1155278C>T
ENST00000675419.1:c.781C>T
ENST00000300305.7:c.781C>T
ENST00000344691.8:c.700C>T
ENST00000358356.9:c.700C>T
ENST00000399237.6:c.745C>T
ENST00000399240.5:c.532+25040C>T
ENST00000437180.5:c.781C>T
ENST00000469087.1:n.317C>T
ENST00000482318.5:c.*371C>T
NM_001001890.2:c.700C>T
NM_001122607.1:c.700C>T
NM_001754.4:c.781C>T
NM_001001890.3:c.700C>T
NM_001122607.2:c.700C>T
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Uncertain Significance

Met criteria codes 1
PM2_Supporting
Not Met criteria codes 25
PM5 PM1 PM3 PM4 PM6 BS2 BS3 BS4 BS1 PVS1 PS2 PS3 PS4 PS1 BP2 BP3 BP4 BP1 BP7 BP5 BA1 PP1 PP4 PP3 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_001754.5(RUNX1):c.781C>T (p.Pro261Ser) is a missense variant, which is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_Supporting). 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: PM2_Supporting.
Met criteria codes
PM2_Supporting
Completely absent from gnomAD v2+v3+v4 with a mean coverage of at least 20X.
Not Met criteria codes
PM5
P261/P234 variants are reported in COSMIC and/or Mastermind, but not at a high enough frequency that they would be likely classified as LP/P.
PM1
Not located at a hotspot (R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R210, R204) or within residues 89-204.
PM3
Not applicable
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No relevant literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
BS2
Not applicable
BS3
No relevant literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
BS4
No relevant literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
BS1
Completely absent from gnomAD v2+v3+v4 with a mean coverage of at least 20X.
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No relevant literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
PS3
No relevant literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
PS4
No relevant literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
Not applicable
BP4
The REVEL score = 0, which is uninformative. SpliceAI doesn't predict any significant splicing impact (Δ scores ≤ 0.20).
BP1
Not applicable
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
Not applicable
BA1
Completely absent from gnomAD v2+v3+v4 with a mean coverage of at least 20X.
PP1
No relevant literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
PP4
Not applicable
PP3
The REVEL score = 0, which is uninformative. SpliceAI doesn't predict any significant splicing impact (Δ scores ≤ 0.20).
PP2
Not applicable
Curation History
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