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.1269C>T (p.Arg423=)

CA10014189

239042 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 35a9e328-f29e-49b8-8ad9-03779bd95996
Approved on: 2019-08-02
Published on: 2019-08-02

HGVS expressions

NM_001754.4:c.1269C>T
NM_001754.4(RUNX1):c.1269C>T (p.Arg423=)
NC_000021.9:g.34792309G>A
CM000683.2:g.34792309G>A
NC_000021.8:g.36164606G>A
CM000683.1:g.36164606G>A
NC_000021.7:g.35086476G>A
NG_011402.2:g.1197403C>T
NM_001001890.2:c.1188C>T
ENST00000300305.7:c.1269C>T
ENST00000344691.8:c.1188C>T
ENST00000399240.5:c.996C>T
ENST00000437180.5:c.1269C>T
ENST00000482318.5:c.*859C>T

Benign

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

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
The MAF for the synonymous variant, NM_001754.4:c.1269C>T (p.Arg423=) is 0.00275 (0.2%, 14/5096 alleles) in the non-Finnish European subpopulation of the ExAC cohort, which is ≥ 0.0015 (0.15%) (BA1). This variant is predicted by SSF and MES to lead to 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 Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP4.
Met criteria codes
BP4
Synonymous variant for which 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.
BA1
ExAC Allele Frequency of European (Non-Finnish) Subpopulation: 0.00275 (14 out of 5096 Alleles) > 0.0015
Not Met criteria codes
BS3
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
BS1
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
BP7
phyloP100way: 0.620126 >0.1
BP2
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
PM6
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
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
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
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