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]

Variant: NM_001754.5(RUNX1):c.1159_1161del (p.Gly387del)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA16616514

409819 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 78031b2f-32da-4fd9-a089-e6bc33bfd63a

Approved on: 2024-08-01

Published on: 2024-08-01

HGVS expressions

NM_001754.5:c.1159_1161del

NM_001754.5(RUNX1):c.1159_1161del (p.Gly387del)

NC_000021.9:g.34792418_34792420del

CM000683.2:g.34792418_34792420del

NC_000021.8:g.36164715_36164717del

CM000683.1:g.36164715_36164717del

NC_000021.7:g.35086585_35086587del

NG_011402.2:g.1197293_1197295del

ENST00000675419.1:c.1159_1161del

ENST00000300305.7:c.1159_1161del

ENST00000344691.8:c.1078_1080del

ENST00000399240.5:c.886_888del

ENST00000437180.5:c.1159_1161del

ENST00000482318.5:c.*749_*751del

NM_001001890.2:c.1078_1080del

NM_001754.4:c.1159_1161del

NM_001001890.3:c.1078_1080del

Uncertain Significance

PM2_Supporting

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

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.1159_1161del (p.Gly387del) is an in-frame deletion which does not affect any residues within the Runt Homology Domain (AA 89-204) (PM4 not applied). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_Supporting). 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: PM2_supporting.

PM2_Supporting

This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_Supporting).

PP1

No case studies found

PP2

This rule is not applicable for MM-VCEP

PP3

No missense, synonymous, or intronic variant

PP4

This rule is not applicable for MM-VCEP

PM6

No case studies found

PM1

Not a missense variant

PM3

This rule is not applicable for MM-VCEP

PM5

This variant is not a missense variant.

PM4

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.

PVS1

This variant is not a null variant.

BA1

This variant does not have a MAF ≥ 0.0015 (0.15%) in any general continental population dataset.

BS2

This rule is not applicable for MM-VCEP

BS1

This variant does not have a MAF between 0.00015 (0.015%) and 0.0015 (0.15%) in any general continental dataset.

BS4

No case studies found

BS3

No functional studies found

BP5

This rule is not applicable for MM-VCEP

BP7

Not a synonymous or intronic variant

BP4

No missense, synonymous, or intronic variant

BP3

This rule is not applicable for MM-VCEP

BP1

This rule is not applicable for MM-VCEP

BP2

No homozygotes present in gnomAD v3.1.2.

PS1

This variant is not a missense variant.

PS2

No case studies found

PS3

No functional studies found

PS4

No case studies found

Curation History

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