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.294C>T (p.Leu98=)

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

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

BP4 BP7

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

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

BP4

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

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).

PS2

nil data

PS4

nil data

PS3

nil data

PS1

not applicable

PP4

not applicable

PP1

nil data

PP3

BP4 met

PP2

not applicable

PM3

not applicable

PM1

not applicable

PM4

not applicable

PM5

not applicable

PM6

nil data

PM2

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

PVS1

not applicable

BA1

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

BS2

not applicable

BS4

not applicable

BS3

nil data

BS1

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

BP2

not applicable

BP3

not applicable

BP1

not applicable

BP5

not applicable

Approved on: 2023-11-13

Published on: 2023-11-13

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