Evidence Repository - Clinical Genome Resources

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

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

Link to MONDO

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

PS4 PS2 PS1 PS3 PVS1 PP4 PP1 PP3 PP2 PM6 PM2 PM5 PM4 PM1 PM3 BA1 BS3 BS4 BS1 BS2 BP5 BP7 BP3 BP2 BP4 BP1

Evidence Links 0

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

PDF

Criteria Specification Approval History

Criteria Specifications for this VCEP

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.

PS4

No case studies found

PS2

No case studies found

PS1

This variant is not a missense variant.

PS3

No functional studies found

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.

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

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

BA1

Variant only present in v2.1.1 and does not meet code criteria (MAF: 0.00002911, 1/34348 in Latino/admixed American subpopulation)

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

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