Variant: NM_001754.5(RUNX1):c.238_243del (p.Glu80_Val81del)

CA10014564

1052786 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

UUID: d8148eec-c53f-40c8-b310-eb5d1f1cc6a3

Approved on: 2024-09-24

Published on: 2024-09-24

HGVS expressions

NM_001754.5:c.238_243del
NM_001754.5(RUNX1):c.238_243del (p.Glu80_Val81del)
NC_000021.9:g.34886955_34886960del
CM000683.2:g.34886955_34886960del
NC_000021.8:g.36259252_36259257del
CM000683.1:g.36259252_36259257del
NC_000021.7:g.35181122_35181127del
NG_011402.2:g.1102756_1102761del
ENST00000675419.1:c.238_243del
ENST00000300305.7:c.238_243del
ENST00000344691.8:c.157_162del
ENST00000358356.9:c.157_162del
ENST00000399237.6:c.202_207del
ENST00000399240.5:c.157_162del
ENST00000437180.5:c.238_243del
ENST00000455571.5:c.199_204del
ENST00000482318.5:c.59-6243_59-6238del
NM_001001890.2:c.157_162del
NM_001122607.1:c.157_162del
NM_001754.4:c.238_243del
NM_001001890.3:c.157_162del
NM_001122607.2:c.157_162del

Uncertain Significance

• Not Met criteria codes: BA1 PM6 PM2 PM5 PM4 PM1 PM3 BS3 BS4 BS1 BS2 BP5 BP7 BP3 BP2 BP4 BP1 PVS1 PS4 PS2 PS1 PS3 PP4 PP1 PP3 PP2

Expert Panel

Myeloid Malignancy VCEP

Criteria Specification Information

Criteria Specification: ClinGen Myeloid Malignancy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

Evidence submitted by expert panel

Myeloid Malignancy VCEP

NM_001754.5(RUNX1):c.238_243del (p.Glu80_Val81del) is an in-frame deletion which does not affect any residues within the Runt Homology Domain (AA 89-204) (PM4 not applied). This variant has not been found in patients meeting the RUNX1 phenotypic criteria. In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: None.

Not Met criteria codes

• BA1: Variant only present in v2.1.1 and does not meet code criteria (MAF: 0.00002911, 1/34348 in Latino/admixed American subpopulation)
• PM6: No case studies found
• PM2: Variant only present in v2.1.1 and does not meet code criteria (MAF: 0.00002911, 1/34348 in Latino/admixed American subpopulation)
• PM5: This variant is not a missense variant.
• PM4: Not an inframe deletion or insertion
• PM1: Not a missense variant
• PM3: This rule is not applicable for MM-VCEP
• BS3: No functional studies found
• BS4: No case studies found
• BS1: Variant only present in v2.1.1 and does not meet code criteria (MAF: 0.00002911, 1/34348 in Latino/admixed American subpopulation)
• BS2: This rule is not applicable for MM-VCEP
• BP5: This rule is not applicable for MM-VCEP
• BP7: Not a synonymous or intronic variant
• BP3: This rule is not applicable for MM-VCEP
• BP2: No homozygotes found in gnomAD v2.1.1
• BP4: Not a missense, synonymous, or intronic variant
• BP1: This rule is not applicable for MM-VCEP
• PVS1: This in-frame deletion/insertion does not affect any of the following amino acid residues, nor is it located within the RHD: R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R201, R204 OR within residues 89-204.
• PS4: No case studies found
• PS2: No case studies found
• PS1: This variant is not a missense variant.
• PS3: No functional studies found
• PP4: This rule is not applicable for MM-VCEP
• PP1: No case studies found
• PP3: Not a missense, synonymous, or intronic variant
• PP2: This rule is not applicable for MM-VCEP