Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: RUNX1 CSPEC Genes: [ 'RUNX1' ] * Message MONDOs: MONDO:0100083 CSPEC MONDO: [ 'MONDO:0011071' ]
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_001754.5(RUNX1):c.*3580T>G

CA10650412

339804 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 8fc36324-ad0d-4371-aad3-4afc8cf17234
Approved on: 2025-01-15
Published on: 2025-01-15

HGVS expressions

NM_001754.5:c.*3580T>G
NM_001754.5(RUNX1):c.*3580T>G
NC_000021.9:g.34788555A>C
CM000683.2:g.34788555A>C
NC_000021.8:g.36160852A>C
CM000683.1:g.36160852A>C
NC_000021.7:g.35082722A>C
NG_011402.2:g.1201157T>G
ENST00000675419.1:c.*3580T>G
ENST00000300305.7:c.*3580T>G
ENST00000344691.8:c.*3580T>G
ENST00000437180.5:c.*3580T>G
NM_001001890.2:c.*3580T>G
NM_001754.4:c.*3580T>G
NM_001001890.3:c.*3580T>G
More

Likely Benign

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

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
NM_001754.5(RUNX1):c.*3580T>G is a 3' UTR variant which has a MAF of 0.00057 (0.057%, 5/8716, alleles) in the African subpopulation of the 20210610 (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 0.00057 (0.057%, 5/8716, alleles) in the African subpopulation of the 20210610 (gnomAD) cohort is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1).
Not Met criteria codes
PP4
Not applicable
PP1
Nil data
PP3
Not applicable
PP2
Not applicable
PVS1
Not applicable
BS4
Nil data
BS3
Nil data
BS2
Not applicable
BP5
Not applicable
BP7
Not applicable
BP2
Not applicable
BP3
Not applicable
BP4
Not applicable
BP1
Not applicable
PM6
Nil data
PM2
BS1 met
PS2
Nil data
PS4
Nil data
PS3
Nil data
PS1
Nil data
BA1
BS1 met
PM3
Not applicable
PM1
Not applicable
PM4
Not applicable
PM5
Nil data
Curation History
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