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.1230G>A (p.Ser410=)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA10014191

578985 (ClinVar)

Gene: RUNX1

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

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 9d246a11-7cf6-47ca-a8ff-34ff19cea26b

Approved on: 2024-06-24

Published on: 2024-06-24

HGVS expressions

NM_001754.5:c.1230G>A

NM_001754.5(RUNX1):c.1230G>A (p.Ser410=)

NC_000021.9:g.34792348C>T

CM000683.2:g.34792348C>T

NC_000021.8:g.36164645C>T

CM000683.1:g.36164645C>T

NC_000021.7:g.35086515C>T

NG_011402.2:g.1197364G>A

ENST00000675419.1:c.1230G>A

ENST00000300305.7:c.1230G>A

ENST00000344691.8:c.1149G>A

ENST00000399240.5:c.957G>A

ENST00000437180.5:c.1230G>A

ENST00000482318.5:c.*820G>A

NM_001001890.2:c.1149G>A

NM_001754.4:c.1230G>A

NM_001001890.3:c.1149G>A

Likely Benign

BP7 BP4

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

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 SpliceAI ∆ scores ≤ 0.20 (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -2.375) (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

PhyloP= -2.375, spliceAI Δ score 0.0 BP7: Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -2.375) (BP7).

BP4

PhyloP= -2.375, spliceAI Δ score 0.0 BP4: This synonymous variant has SpliceAI ∆ scores ≤ 0.20

BS4

Nil data

BS3

Nil data

BS1

GnomAD V2: European (Non-Finnish) 2/63492 alleles (0.00003)

BS2

Nil data

BP5

not applicable

BP2

not applicable

BP3

Synonymous variant

BP1

synonymous variant

PS2

Nil data

PS4

Nil data

PS3

Nil data

PS1

synonymous variant

PVS1

synonymous variant

PP4

not applicable

PP1

Nil data

PP3

synonymous variant

PP2

synonymous variant

PM3

not applicable

PM1

Nil data

PM4

Synonymous variant

PM5

synonymous variant

PM6

Nil data

PM2

GnomAD V2: European (Non-Finnish) 2/63492 alleles (0.00003)

BA1

GnomAD V2: European (Non-Finnish) 2/63492 alleles (0.00003)

Curation History

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