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.294C>T (p.Leu98=)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA512318849

1561682 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 26351632-009c-4df9-adce-268e4032a3c2

Approved on: 2023-11-13

Published on: 2023-11-13

HGVS expressions

NM_001754.5:c.294C>T

NM_001754.5(RUNX1):c.294C>T (p.Leu98=)

NC_000021.9:g.34886900G>A

CM000683.2:g.34886900G>A

NC_000021.8:g.36259197G>A

CM000683.1:g.36259197G>A

NC_000021.7:g.35181067G>A

NG_011402.2:g.1102812C>T

ENST00000675419.1:c.294C>T

ENST00000300305.7:c.294C>T

ENST00000344691.8:c.213C>T

ENST00000358356.9:c.213C>T

ENST00000399237.6:c.258C>T

ENST00000399240.5:c.213C>T

ENST00000437180.5:c.294C>T

ENST00000455571.5:c.255C>T

ENST00000482318.5:c.59-6187C>T

NM_001001890.2:c.213C>T

NM_001122607.1:c.213C>T

NM_001754.4:c.294C>T

NM_001001890.3:c.213C>T

NM_001122607.2:c.213C>T

Likely Benign

BP7 BP4

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

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

BP4 Multiple lines of computational evidence suggest no impact on gene /gene product. BP4: This synonymous variant has a SpliceAI Δ score < 0.2 and PhyloP100way: 1.191 BP7 Silent variant predicted with no splice impact. BP7: Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score < 2.0) (BP7). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7

BP7

SpliceAI Δ score < 0.2 PhyloP100way: 1.191 BP7: Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score < 2.0) (BP7).

BP4

SpliceAI Δ score < 0.2 PhyloP100way: 1.191 BP4: This synonymous variant has a SpliceAI Δ score < 0.2 and PhyloP100way: 1.191

PVS1

not applicable

PS2

nil data

PS4

nil data

PS3

nil data

PS1

not applicable

BA1

gnomAD V2: not present, gnomAD V3: ƒ = 0.00000657

PP4

not applicable

PP1

nil data

PP3

BP4 met

PP2

not applicable

PM6

nil data

PM2

gnomAD V2: not present, gnomAD V3: ƒ = 0.00000657

PM3

not applicable

PM1

not applicable

PM4

not applicable

PM5

not applicable

BS4

not applicable

BS3

nil data

BS1

gnomAD V2: not present, gnomAD V3: ƒ = 0.00000657

BS2

not applicable

BP5

not applicable

BP2

not applicable

BP3

not applicable

BP1

not applicable

Curation History

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