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.805+12836A>G

CA14892082

1260410 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: dda1735c-9240-46d0-a84c-6a98b2f8cf0b
Approved on: 2024-11-04
Published on: 2024-11-04

HGVS expressions

NM_001754.5:c.805+12836A>G
NM_001754.5(RUNX1):c.805+12836A>G
NC_000021.9:g.34821574T>C
CM000683.2:g.34821574T>C
NC_000021.8:g.36193871T>C
CM000683.1:g.36193871T>C
NC_000021.7:g.35115741T>C
NG_011402.2:g.1168138A>G
ENST00000675419.1:c.805+12836A>G
ENST00000300305.7:c.805+12836A>G
ENST00000344691.8:c.724+12836A>G
ENST00000358356.9:c.*94A>G
ENST00000399240.5:c.533-22112A>G
ENST00000437180.5:c.805+12836A>G
ENST00000479325.1:n.242A>G
ENST00000482318.5:c.*395+12836A>G
NM_001001890.2:c.724+12836A>G
NM_001122607.1:c.*94A>G
NM_001754.4:c.805+12836A>G
NM_001001890.3:c.724+12836A>G
NM_001122607.2:c.*94A>G
More

Benign

Met criteria codes 4
BA1 BP4 BP2 BP7
Not Met criteria codes 22
PS4 PS2 PS1 PS3 PP1 PP3 PP2 PP4 PM6 PM2 PVS1 PM5 PM1 PM4 PM3 BS2 BS4 BS3 BS1 BP1 BP3 BP5

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
The NM_001754.5(RUNX1):c.805+12836A>G variant is a deep intronic variant that is not predicted by SpliceAI to impact splicing (BP4). The variant's highest minor allele frequency (MAF) of 0.9987(99.87%, 1156/1558 alleles) in the East Asian subpopulation of the gnomADv2.1.1 cohort is ≥ 0.0015 (0.15%) (BP1). Additionally this variant is detected in a homozygous state in 777 individuals in a population database (gnomADv2.1.1) (BP2). This deep intronic variant is not well conserved with a phyloP100way score of -0.014 (BP7 ≤2.0). It has not been reported in individuals meeting at least one of the RUNX1 phenotypic criteria. In summary, the clinical significance of this variant is Benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4, BP7.
Met criteria codes
BA1
MAF of 0.9987(99.87%, 1156/1558 alleles) in the East Asian subpopulation of the gnomADv2.1.1 cohort is ≥ 0.0015 (0.15%) (BA1).
BP4
SpliceAI score of 0
BP2
This variant is detected in a homozygous state in 777 individual in a population database (gnomADv2.1.1). (BP2)
BP7
This intronic variant has a SpliceAI score of zero and is not well conserved with a phyloP100way score of -0.014 (BP7 ≤2.0)
Not Met criteria codes
PS4
No case study found
PS2
No case study found
PS1
No amino acid change
PS3
No studies found
PP1
No case study found
PP3
Not a missense variant
PP2
This rule is not applicable for MM-VCEP
PP4
This rule is not applicable for MM-VCEP
PM6
No case study found
PM2
BA1 met
PVS1
Not a null variant
PM5
not a missense variant
PM1
Not located in known mutational hot spot or established functional domain
PM4
No protein length change is predicted
PM3
This rule is not applicable for MM-VCEP
BS2
This rule is not applicable for MM-VCEP
BS4
No case study found
BS3
No studies found
BS1
BA1 met
BP1
This rule is not applicable for MM-VCEP
BP3
This rule is not applicable for MM-VCEP
BP5
This rule is not applicable for MM-VCEP
Curation History
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