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.939_950del (p.Ala315_Ser318del)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA10014262

532672 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: f763c5bc-f2eb-4f88-b7a2-b4ab82c26df2

Approved on: 2024-08-01

Published on: 2024-08-01

HGVS expressions

NM_001754.5:c.939_950del

NM_001754.5(RUNX1):c.939_950del (p.Ala315_Ser318del)

NC_000021.9:g.34799320_34799331del

CM000683.2:g.34799320_34799331del

NC_000021.8:g.36171617_36171628del

CM000683.1:g.36171617_36171628del

NC_000021.7:g.35093487_35093498del

NG_011402.2:g.1190383_1190394del

ENST00000675419.1:c.939_950del

ENST00000300305.7:c.939_950del

ENST00000344691.8:c.858_869del

ENST00000399240.5:c.666_677del

ENST00000437180.5:c.939_950del

ENST00000482318.5:c.*529_*540del

NM_001001890.2:c.858_869del

NM_001754.4:c.939_950del

NM_001001890.3:c.858_869del

Likely Benign

BS1

BA1 PM1 PM5 PM3 PM4 PM6 PM2 PS2 PS3 PS4 PS1 PP1 PP4 PP3 PP2 PVS1 BS2 BS4 BS3 BP2 BP3 BP4 BP1 BP7 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.939_950del (p.Ala315_Ser318del) is an in-frame deletion which does not occur within the Runt Homology Domain (AA 89-204) (PM4 not applied). This variant has a MAF of 0.0001858 (0.01858%, 24/129186, 24 alleles) in the European (non-Finnish) subpopulation of the gnomAD cohort, which is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). 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.

BS1

MAF of 0.0001858 (0.01858%, 24/129186, 24 alleles) in the European (non-Finnish) subpopulation of the gnomAD cohort is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1).

BA1

MAF of 0.0001858 (0.01858%, 24/129186, 24 alleles) in the European (non-Finnish) subpopulation of the gnomAD cohort is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1).

PM1

Not a missense variant

PM5

Not a missense variant

PM3

This rule is not applicable for MM-VCEP

PM4

This in-frame deletion/insertion does not affect any of the following amino acid residues, nor is it located within the RHD: R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R201, R204 OR within residues 89-204.

PM6

No case studies found

PM2

MAF of 0.0001858 (0.01858%, 24/129186, 24 alleles) in the European (non-Finnish) subpopulation of the gnomAD cohort is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1).

PS2

No case studies found

PS3

No functional studies found

PS4

Cannot be applied as the variant meets BS1

PS1

Not a missense variant

PP1

No case studies found

PP4

This rule is not applicable for MM-VCEP

PP3

Not a missense variant

PP2

This rule is not applicable for MM-VCEP

PVS1

This variant is not a null variant.

BS2

This rule is not applicable for MM-VCEP

BS4

No case studies found

BS3

No functional studies found

BP2

No homozygotes present in gnomAD v2.1.1 or v3.1.2

BP3

This rule is not applicable for MM-VCEP

BP4

Not a missense variant

BP1

This rule is not applicable for MM-VCEP

BP7

Not a synonymous of intronic variant

BP5

The rule is not applicable for the MM-VCEP

Curation History

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