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.155T>A (p.Met52Lys)

CA10014581

239044 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 4ceacdfa-56c1-4933-a48a-f8c97e4f92e9

HGVS expressions

NM_001754.4:c.155T>A
NM_001754.4(RUNX1):c.155T>A (p.Met52Lys)
NC_000021.9:g.34887039A>T
CM000683.2:g.34887039A>T
NC_000021.8:g.36259336A>T
CM000683.1:g.36259336A>T
NC_000021.7:g.35181206A>T
NG_011402.2:g.1102673T>A
NM_001001890.2:c.74T>A
NM_001122607.1:c.74T>A
ENST00000300305.7:c.155T>A
ENST00000344691.8:c.74T>A
ENST00000358356.9:c.74T>A
ENST00000399237.6:c.119T>A
ENST00000399240.5:c.74T>A
ENST00000437180.5:c.155T>A
ENST00000455571.5:c.116T>A
ENST00000482318.5:c.59-6326T>A

Uncertain Significance

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

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
The NM_001754.4:c.155T>A (p.Met52Lys) variant has a MAF of 0.00071 (0.071%, 6/8,456 alleles) in the EA Allele subpopulation of the ESP cohort that is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). This missense variant has a REVEL score >0.75 (0.845) (PP3). In summary, the clinical significance of this variant is uncertain (VUS). ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BS1, PP3.
Met criteria codes
PP3
REVEL: 0.845 >0.75
BS1
EA Allele Subpopulation of ESP Allele Frequency (6 out of 8456 alleles): 0.00071 > 0.00015
Not Met criteria codes
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
1 proband, but PS4 can not apply in combined with BS1
Pt 9 with AML, germline variant on cultured skin fibroblasts PubMed:29365323
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
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
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
EA Allele Subpopulation of ESP Allele Frequency (6 out of 8456 alleles): 0.00071 < 0.0015
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
PVS1
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
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2019-07-26
Published on: 2019-08-02
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