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.1071G>A (p.Pro357=)

CA512341330

2146447 (ClinVar)

Gene: RUNX1 (HGNC:861)

Condition: hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 (MONDO:0100083)

Inheritance Mode: Autosomal dominant inheritance

UUID: 89d87f97-5584-481e-9d7b-61d6e8fd11c5

Approved on: 2024-06-24

Published on: 2024-06-24

HGVS expressions

NM_001754.5(RUNX1):c.1071G>A (p.Pro357=)

NM_001754.5:c.1071G>A

NC_000021.9:g.34792507C>T

CM000683.2:g.34792507C>T

NC_000021.8:g.36164804C>T

CM000683.1:g.36164804C>T

NC_000021.7:g.35086674C>T

NG_011402.2:g.1197205G>A

ENST00000675419.1:c.1071G>A

ENST00000300305.7:c.1071G>A

ENST00000344691.8:c.990G>A

ENST00000399240.5:c.798G>A

ENST00000437180.5:c.1071G>A

ENST00000482318.5:c.*661G>A

NM_001001890.2:c.990G>A

NM_001754.4:c.1071G>A

NM_001001890.3:c.990G>A

Likely Benign

BP4 BP7

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

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 synonymous variant has a SpliceAI Δ score of 0.00 (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.008 (< 2)) (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

PhyloP100way= -3.096 Splice AI Δ score = 0.00 BP4: This synonymous variant has a Splice AI Δ score = 0.00

BP7

PhyloP100way= -3.096 Splice AI Δ score = 0.00 BP7: Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -3.096 (< 2.0) or the variant is the reference nucleotide in one primate and/or three mammal species) (BP7).

PM3

not applicable

PM1

not applicable

PM4

Not applicable

PM5

not applicable

PM6

nil data

PM2

allele frequency 0.00000911 (gnomAD Version: 20210610)

BS2

not applicable

BS4

nil data

BS3

nil data

BS1

allele frequency 0.00000911 (gnomAD Version: 20210610)

PVS1

not applicable

PS2

nil data

PS4

nil data

PS3

nil data

PS1

not applicable

BP2

not applicable

BP3

Not applicable

BP1

not applicable

BP5

not applicable

BA1

allele frequency 0.00000911 (gnomAD Version: 20210610)

PP4

not applicable

PP1

nil data

PP3

PhyloP100way= -3.096 Splice AI Δ score = 0.00

PP2

not applicable

Curation History

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