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.351+10C>T

CA10014546

1094393 (ClinVar)

Gene: RUNX1

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

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: da519a08-4d94-4c6f-8ac5-e9534b885313

Approved on: 2024-06-24

Published on: 2024-06-24

HGVS expressions

NM_001754.5:c.351+10C>T

NM_001754.5(RUNX1):c.351+10C>T

NC_000021.9:g.34886833G>A

CM000683.2:g.34886833G>A

NC_000021.8:g.36259130G>A

CM000683.1:g.36259130G>A

NC_000021.7:g.35181000G>A

NG_011402.2:g.1102879C>T

ENST00000675419.1:c.351+10C>T

ENST00000300305.7:c.351+10C>T

ENST00000344691.8:c.270+10C>T

ENST00000358356.9:c.270+10C>T

ENST00000399237.6:c.315+10C>T

ENST00000399240.5:c.270+10C>T

ENST00000437180.5:c.351+10C>T

ENST00000455571.5:c.312+10C>T

ENST00000482318.5:c.59-6120C>T

NM_001001890.2:c.270+10C>T

NM_001122607.1:c.270+10C>T

NM_001754.4:c.351+10C>T

NM_001001890.3:c.270+10C>T

NM_001122607.2:c.270+10C>T

Likely Benign

BP7 BP4 BS1

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

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 has a MAF of 0.0002513 (0.02513%, 5/19896 alleles) in the East Asian subpopulation of the gnomAD V2 cohort, which is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). This intronic variant has a SpliceAI ∆ score ≤ 0.20 (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.49) (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: BS1, BP4, BP7.

BP7

Splice AI score 0.0 PhyloP -0.49 BP7: Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.49 (BP7)).

BP4

intronic variant SpliceAI not predictive of novel splice site creation (score 0.0) BP4: This intronic variant has a SpliceAI ∆ scores ≤ 0.20

BS1

MAF of 0.0002513 (0.02513%, 5/19896 alleles) in the East Asian subpopulation of the gnomAD V2 cohort is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1).

PP4

not applicable

PP1

nil data

PP3

intronic variant not applicable

PP2

not applicable

PM3

not applicable

PM1

nil data

PM4

Intronic variant not applicable

PM5

Intronic variant not applicable

PS2

nil data

PS4

nil data, BS1 met

PS3

nil data

PS1

Intronic variant not applicable

PM6

nil data

PM2

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BA1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PVS1

Intronic variant not applicable

BP5

not applicable

BP2

not applicable

BP3

Intronic variant not applicable

BP1

not applicable

BS2

nil data

BS4

nil data

BS3

nil data

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