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

CA10014262

532672 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
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
More

Likely Benign

Met criteria codes 1
BS1
Not Met criteria codes 25
PVS1 BS4 BS3 BS2 BP7 BP5 BP2 BP3 BP4 BP1 PS2 PS3 PS4 PS1 BA1 PP1 PP4 PP3 PP2 PM1 PM5 PM3 PM4 PM6 PM2

Evidence Links 0

Expert Panel

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.
Met criteria codes
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).
Not Met criteria codes
PVS1
This variant is not a null variant.
BS4
No case studies found
BS3
No functional studies found
BS2
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
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
PS2
No case studies found
PS3
No functional studies found
PS4
Cannot be applied as the variant meets BS1
PS1
Not a missense variant
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).
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
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).
Curation History
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