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]
Link to SEPIO compliant JSON-LD document
  • See Evidence submitted by expert panel for details.

Variant: NM_001754.4(RUNX1):c.614-34C>T

CA10014405

258186 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: e7c466ba-2630-4273-adcf-da7d8ca99b52
Approved on: 2019-07-26
Published on: 2019-08-02

HGVS expressions

NM_001754.4:c.614-34C>T
NM_001754.4(RUNX1):c.614-34C>T
NC_000021.9:g.34834635G>A
CM000683.2:g.34834635G>A
NC_000021.8:g.36206932G>A
CM000683.1:g.36206932G>A
NC_000021.7:g.35128802G>A
NG_011402.2:g.1155077C>T
NM_001001890.2:c.533-34C>T
NM_001122607.1:c.533-34C>T
ENST00000300305.7:c.614-34C>T
ENST00000344691.8:c.533-34C>T
ENST00000358356.9:c.533-34C>T
ENST00000399237.6:c.578-34C>T
ENST00000399240.5:c.532+24839C>T
ENST00000437180.5:c.614-34C>T
ENST00000469087.1:n.150-34C>T
ENST00000482318.5:c.*204-34C>T

Benign

Met criteria codes 3
BA1 BP2 BP4
Not Met criteria codes 15
BP7 BS4 BS1 BS3 PVS1 PP1 PP3 PM5 PM1 PM4 PM6 PM2 PS4 PS1 PS3

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.614-34C>T variant has a MAF of 1 (100%) in gnomAD cohort that is ≥ 0.0015 (0.15%) (BA1). This variant is detected in homozygous state in gnomAD population database (BP2). This intronic variant is predicted by SSF and MES to lead to 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, ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4.
Met criteria codes
BA1
gnomAD Allele Frequency: 1
BP2
This variant is detected in homozygous state in gnomAD population database.
BP4
Intronic 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.
Not Met criteria codes
BP7
phyloP100way: 1.06724 >0.1
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
BS3
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
PP1
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
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
PM4
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
PS4
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
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