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.563C>G (p.Thr188Ser)

CA410208042

532659 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia with normal platelets-hematological cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: cf85a4a4-1e5d-4f72-b064-0a7bbcc1e78e
Approved on: 2019-07-26
Published on: 2019-08-02

HGVS expressions

NM_001754.4:c.563C>G
NM_001754.4(RUNX1):c.563C>G (p.Thr188Ser)
NC_000021.9:g.34859524G>C
CM000683.2:g.34859524G>C
NC_000021.8:g.36231821G>C
CM000683.1:g.36231821G>C
NC_000021.7:g.35153691G>C
NG_011402.2:g.1130188C>G
NM_001001890.2:c.482C>G
NM_001122607.1:c.482C>G
ENST00000300305.7:c.563C>G
ENST00000344691.8:c.482C>G
ENST00000358356.9:c.482C>G
ENST00000399237.6:c.527C>G
ENST00000399240.5:c.482C>G
ENST00000437180.5:c.563C>G
ENST00000467577.1:n.55C>G
ENST00000482318.5:c.*153C>G

Uncertain Significance

Met criteria codes 3
PM1_Supporting PP3 PM2
Not Met criteria codes 15
PVS1 BA1 BS3 BS1 BS4 BP4 BP2 BP7 PS1 PS3 PS4 PP1 PM6 PM5 PM4

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.563C>G (p.Thr188Ser) variant affects one of the residues (AA 105-204) within the RHD (PM1_Supporting). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2). This missense variant has a REVEL score >0.75 (0.922) (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: PM2, PP3, PM1_supporting.
Met criteria codes
PM1_Supporting
Residue in RUNT domain (105-204aa).
PP3
REVEL: 0.922 >0.75
PM2
The variant is absent from all population databases.
Not Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
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
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
BP7
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
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
PM5
p.Thr188Ile may be deleterious. PM5 needs to be reviewed again after the curation of p.Thr188Ile is done.
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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