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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  • See Evidence submitted by expert panel for details.

Variant: NM_001754.4(RUNX1):c.824C>T (p.Pro275Leu)

CA10014287

464009 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ed562b68-0918-4a40-899c-7000d16d5da8
Approved on: 2019-08-02
Published on: 2019-08-02

HGVS expressions

NM_001754.4:c.824C>T
NM_001754.4(RUNX1):c.824C>T (p.Pro275Leu)
NC_000021.9:g.34799444G>A
CM000683.2:g.34799444G>A
NC_000021.8:g.36171741G>A
CM000683.1:g.36171741G>A
NC_000021.7:g.35093611G>A
NG_011402.2:g.1190268C>T
NM_001001890.2:c.743C>T
ENST00000300305.7:c.824C>T
ENST00000344691.8:c.743C>T
ENST00000399240.5:c.551C>T
ENST00000437180.5:c.824C>T
ENST00000482318.5:c.*414C>T

Benign

Met criteria codes 2
BA1 BP4
Not Met criteria codes 16
PM5 PM4 PM1 PM2 PM6 BS3 BS1 BS4 BP2 BP7 PVS1 PS1 PS3 PS4 PP3 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
The NM_001754.4:c.824C>T (p.Pro275Leu) variant has an MAF of 0.00225 (0.2%, 26/11566 alleles) in the Latino subpopulation of the ExAC cohort that is ≥ 0.0015 (0.15%) (BA1). This missense variant has a REVEL score <0.15 (0.146) and SSF and MES predict 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 summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP4.
Met criteria codes
BA1
ExAC Allele Frequency of Latino Subpopulation: 0.00225 (26 out of 11566 Alleles) > 0.0015
BP4
REVEL: 0.146 <0.15 AND agreement in splicing predictors (SSF and MES) predict no splicing effects.
Not Met criteria codes
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
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
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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