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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Curation History
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CA14902396

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 1ea15ebf-9b71-4bab-9317-612167c8d83a

Approved on: 2024-06-24

Published on: 2024-06-24

HGVS expressions

NM_001754.5:c.98-1560C>T

NC_000021.9:g.34888656G>A

CM000683.2:g.34888656G>A

NC_000021.8:g.36260953G>A

CM000683.1:g.36260953G>A

NC_000021.7:g.35182823G>A

NG_011402.2:g.1101056C>T

ENST00000675419.1:c.98-1560C>T

ENST00000300305.7:c.98-1560C>T

ENST00000344691.8:c.-1544C>T

ENST00000358356.9:c.-1544C>T

ENST00000399237.6:c.61+1021C>T

ENST00000437180.5:c.98-1560C>T

ENST00000455571.5:c.59-1560C>T

ENST00000475045.6:c.98-1560C>T

ENST00000482318.5:c.59-7943C>T

NM_001001890.2:c.-1544C>T

NM_001122607.1:c.-1544C>T

NM_001754.4:c.98-1560C>T

NM_001001890.3:c.-1544C>T

NM_001122607.2:c.-1544C>T

Benign

BA1 BP2 BP4 BP7

PM4 PM5 PM1 PM3 PM6 PM2 PS1 PS2 PS3 PS4 PP4 PP1 PP3 PP2 PVS1 BS2 BS4 BS3 BS1 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

PDF

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

NM_001754.5(RUNX1):c.98-1560C>T is an intronic variant. MAF of 0.0.05199 (5.19%, 251/1328, 4828 alleles) in the South Asian subpopulation of the gnomAD v3.1.2 cohort is ≥ 0.0015 (0.15%) (BA1). There are 12 homozygotes present in gnomAD v3.1.2 (BP2). This variant is not a missense variant therefore will not have a REVEL score and SpliceAI score <0.20 (0.00) (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 0.82 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species) (BP7). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4, BP7.

BA1

MAF of 0.0.05199 (5.19%, 251/1328, 4828 alleles) in the South Asian subpopulation of the gnomAD v3.1.2 cohort is ≥ 0.0015 (0.15%).

BP2

There are 12 homozygotes present in gnomAD v3.1.2.

BP4

This variant is not a missense variant therefore will not have a REVEL score and SpliceAI score <0.20 (0.00)

BP7

Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 0.82 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species)

PM4

Not a FS variant

PM5

Not a missense variant

PM1

Not a missense variant

PM3

This rule is not applicable for MM-VCEP

PM6

Meets BA1

PM2

Meets BA1

PS1

Not a missense variant

PS2

Meets BA1

PS3

No functional studies found

PS4

Meets BA1

PP4

This rule is not applicable for MM-VCEP

PP1

Meets BA1

PP3

This variant is not a missense variant therefore will not have a REVEL score and SpliceAI score <0.20 (0.00)

PP2

This rule is not applicable for MM-VCEP

PVS1

Not a null variant

BS2

This rule is not applicable for MM-VCEP

BS4

Meets BA1

BS3

No functional studies found

BS1

Meets BA1

BP3

This rule is not applicable for MM-VCEP

BP1

This rule is not applicable for MM-VCEP

BP5

This rule is not applicable for MM-VCEP

Curation History

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