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


CA14902396

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 1ea15ebf-9b71-4bab-9317-612167c8d83a
Approved on: 2024-06-24
Published on: 2024-06-24

HGVS expressions

NM_001754.5:c.98-1560C>T
NC_000021.9:g.34888656G>A
CM000683.2:g.34888656G>A
NC_000021.8:g.36260953G>A
CM000683.1:g.36260953G>A
NC_000021.7:g.35182823G>A
NG_011402.2:g.1101056C>T
ENST00000675419.1:c.98-1560C>T
ENST00000300305.7:c.98-1560C>T
ENST00000344691.8:c.-1544C>T
ENST00000358356.9:c.-1544C>T
ENST00000399237.6:c.61+1021C>T
ENST00000437180.5:c.98-1560C>T
ENST00000455571.5:c.59-1560C>T
ENST00000475045.6:c.98-1560C>T
ENST00000482318.5:c.59-7943C>T
NM_001001890.2:c.-1544C>T
NM_001122607.1:c.-1544C>T
NM_001754.4:c.98-1560C>T
NM_001001890.3:c.-1544C>T
NM_001122607.2:c.-1544C>T
More

Benign

Met criteria codes 4
BP7 BP2 BP4 BA1
Not Met criteria codes 22
PVS1 BS4 BS3 BS1 BS2 BP5 BP3 BP1 PS1 PS2 PS3 PS4 PP4 PP1 PP3 PP2 PM4 PM5 PM1 PM3 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.98-1560C>T is an intronic variant. MAF of 0.0.05199 (5.19%, 251/1328, 4828 alleles) in the South Asian subpopulation of the gnomAD v3.1.2 cohort is ≥ 0.0015 (0.15%) (BA1). There are 12 homozygotes present in gnomAD v3.1.2 (BP2). This variant is not a missense variant therefore will not have a REVEL score and SpliceAI score <0.20 (0.00) (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 0.82 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species) (BP7). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4, BP7.
Met criteria codes
BP7
Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 0.82 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species)
BP2
There are 12 homozygotes present in gnomAD v3.1.2.
BP4
This variant is not a missense variant therefore will not have a REVEL score and SpliceAI score <0.20 (0.00)
BA1
MAF of 0.0.05199 (5.19%, 251/1328, 4828 alleles) in the South Asian subpopulation of the gnomAD v3.1.2 cohort is ≥ 0.0015 (0.15%).
Not Met criteria codes
PVS1
Not a null variant
BS4
Meets BA1
BS3
No functional studies found
BS1
Meets BA1
BS2
This rule is not applicable for MM-VCEP
BP5
This rule is not applicable for MM-VCEP
BP3
This rule is not applicable for MM-VCEP
BP1
This rule is not applicable for MM-VCEP
PS1
Not a missense variant
PS2
Meets BA1
PS3
No functional studies found
PS4
Meets BA1
PP4
This rule is not applicable for MM-VCEP
PP1
Meets BA1
PP3
This variant is not a missense variant therefore will not have a REVEL score and SpliceAI score <0.20 (0.00)
PP2
This rule is not applicable for MM-VCEP
PM4
Not a FS variant
PM5
Not a missense variant
PM1
Not a missense variant
PM3
This rule is not applicable for MM-VCEP
PM6
Meets BA1
PM2
Meets BA1
Curation History
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