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
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001754.5(RUNX1):c.*3417A>G

CA10653549

339808 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: b2a548a9-9fba-4673-9b10-36d59c099869
Approved on: 2025-01-15
Published on: 2025-01-15

HGVS expressions

NM_001754.5:c.*3417A>G
NM_001754.5(RUNX1):c.*3417A>G
NC_000021.9:g.34788718T>C
CM000683.2:g.34788718T>C
NC_000021.8:g.36161015T>C
CM000683.1:g.36161015T>C
NC_000021.7:g.35082885T>C
NG_011402.2:g.1200994A>G
ENST00000675419.1:c.*3417A>G
ENST00000300305.7:c.*3417A>G
ENST00000344691.8:c.*3417A>G
ENST00000437180.5:c.*3417A>G
NM_001001890.2:c.*3417A>G
NM_001754.4:c.*3417A>G
NM_001001890.3:c.*3417A>G
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Likely Benign

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

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
NM_001754.5(RUNX1):c.*3417A>G is a 3' UTR variant which has a MAF of 0.0001764 (0.01764%, 12/68008, 12 alleles) in the European (non-Finnish) subpopulation of the gnomAD v4 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 0.0001764 (0.01764%, 12/68008, 12 alleles) in the European (non-Finnish) subpopulation of the gnomAD v4 cohort is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1).
Not Met criteria codes
BS2
This rule is not applicable for MM-VCEP.
BS4
Segregation data for this variant has not been reported in literature.
BS3
In vitro or in vivo functional data has not been reported for this variant in the literature.
BP2
This variant has not been observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
BP3
This rule is not applicable for MM-VCEP.
BP4
This variant does not have applicable in-silico data available.
BP1
This rule is not applicable for MM-VCEP.
BP7
This variant is not a synonymous or intronic variant.
BP5
This rule is not applicable for MM-VCEP.
BA1
This variant does not have a MAF ≥ 0.0015 (0.15%) in any general continental population dataset.
PS2
De novo data for this variant has not been reported in literature.
PS4
Proband data for this variant has not been reported in literature.
PS3
In vitro or in vivo functional data has not been reported for this variant in the literature.
PS1
This variant is not a missense variant.
PP1
Segregation data for this variant has not been reported in literature.
PP4
This rule is not applicable for MM-VCEP.
PP3
This variant does not have applicable in-silico data available.
PP2
This rule is not applicable for MM-VCEP.
PVS1
This variant is not a null variant.
PM1
This variant is not a missense variant.
PM5
This variant is not a missense variant.
PM3
This rule is not applicable for MM-VCEP.
PM4
This variant is not an in-frame deletion/insertion.
PM6
De novo data for this variant has not been reported in literature.
PM2
This variant is present in at least one population database.
Curation History
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