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]

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Variant: NM_001754.5(RUNX1):c.97+4T>C

CA512319027

532674 (ClinVar)

Gene: RUNX1

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

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 4dfb2352-1b37-4417-a444-f348d3901399

Approved on: 2024-06-24

Published on: 2024-06-24

HGVS expressions

NM_001754.5:c.97+4T>C

NM_001754.5(RUNX1):c.97+4T>C

NC_000021.9:g.34892921A>G

CM000683.2:g.34892921A>G

NC_000021.8:g.36265218A>G

CM000683.1:g.36265218A>G

NC_000021.7:g.35187088A>G

NG_011402.2:g.1096791T>C

ENST00000675419.1:c.97+4T>C

ENST00000300305.7:c.97+4T>C

ENST00000437180.5:c.97+4T>C

ENST00000455571.5:c.59-5825T>C

ENST00000475045.6:c.97+4T>C

ENST00000482318.5:c.59-12208T>C

NM_001754.4:c.97+4T>C

Likely Benign

BP7 BP4 PM2_Supporting

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

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

This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting). This intronic variant has a Splice AI Δ scores < 0.2 (BP4, BP7). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 0.662) (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: PM2_supporting, BP4, BP7

BP7

phyloP100: 0.662 All Splice AI Δ scores < 0.2 BP7: Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 0.662) (BP7).

BP4

All Splice AI Δ scores < 0.2 BP4: This intronic variant has a Splice AI Δ scores < 0.2

PM2_Supporting

This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting).

PVS1

not applicable

BA1

Absent from gnomAD V2 and V3

BP5

not applicable

BP2

not applicable

BP1

not applicable

BP3

not applicable

BS4

nil data

BS3

nil data

BS1

Absent from gnomAD V2 and V3

BS2

nil data

PP4

not applicable

PP1

nil data

PP3

All Splice AI Δ scores < 0.2

PP2

not applicable

PM3

not applicable

PM1

nil data

PM5

not applicable

PM4

not applicable

PS2

nil data

PS4

nil data

PS3

nil data

PS1

not applicable

PM6

nil data

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