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

Variant: NM_001754.5(RUNX1):c.303G>T (p.Val101=)

CA10014552

239047 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 997ae198-ae6a-441e-98eb-97f297cbc204
Approved on: 2024-06-24
Published on: 2024-06-24

HGVS expressions

NM_001754.5:c.303G>T
NM_001754.5(RUNX1):c.303G>T (p.Val101=)
NC_000021.9:g.34886891C>A
CM000683.2:g.34886891C>A
NC_000021.8:g.36259188C>A
CM000683.1:g.36259188C>A
NC_000021.7:g.35181058C>A
NG_011402.2:g.1102821G>T
ENST00000675419.1:c.303G>T
ENST00000300305.7:c.303G>T
ENST00000344691.8:c.222G>T
ENST00000358356.9:c.222G>T
ENST00000399237.6:c.267G>T
ENST00000399240.5:c.222G>T
ENST00000437180.5:c.303G>T
ENST00000455571.5:c.264G>T
ENST00000482318.5:c.59-6178G>T
NM_001001890.2:c.222G>T
NM_001122607.1:c.222G>T
NM_001754.4:c.303G>T
NM_001001890.3:c.222G>T
NM_001122607.2:c.222G>T
More

Benign

Met criteria codes 3
BA1 BP4 BP7
Not Met criteria codes 23
PM6 PM2 PM1 PM4 PM5 PM3 BS2 BS4 BS3 BS1 BP3 BP2 BP1 BP5 PS2 PS4 PS3 PS1 PVS1 PP1 PP4 PP3 PP2

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.303G>T (p.Val101=) is a synonymous variant. MAF of 0.00671 (0.671%, 167/24878, 167 alleles) in the African subpopulation of the gnomAD cohort is ≥ 0.0015 (0.15%) (BA1). Not a missense variant, therefore, no REVEL score and SpliceAI is ≤0.50 (0.00) (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 1.4739 < 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, BP4, BP7.
Met criteria codes
BA1
MAF of 0.00671 (0.671%, 167/24878, 167 alleles) in the African subpopulation of the gnomAD cohort is ≥ 0.0015 (0.15%) (BA1).
BP4
Not a missense variant, therefore, no REVEL score and SpliceAI is ≤0.50 (0.00) (BP4)
BP7
Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score 1.4739 < 2.0 or the variant is the reference nucleotide in one primate and/or three mammal species) (BP7).
Not Met criteria codes
PM6
No case studies found
PM2
MAF of 0.00671 (0.671%, 167/24878, 167 alleles) in the African subpopulation of the gnomAD cohort is ≥ 0.0015 (0.15%) (BA1).
PM1
Not a missense variant
PM4
Not an in-frame deletion/insertion
PM5
Not a missense variant
PM3
This rule is not applicable for MM-VCEP
BS2
This rule is not applicable for MM-VCEP
BS4
No case studies found
BS3
No functional studies found
BS1
MAF of 0.00671 (0.671%, 167/24878, 167 alleles) in the African subpopulation of the gnomAD cohort is ≥ 0.0015 (0.15%) (BA1).
BP3
This rule is not applicable for MM-VCEP
BP2
No homozygotes found in gnomAD
BP1
This rule is not applicable for MM-VCEP
BP5
This rule is not applicable for MM-VCEP
PS2
No case studies found
PS4
No case studies found
PS3
No functional studies found
PS1
Not a missense variant
PVS1
Not a null variant
PP1
No case studies found
PP4
This rule is not applicable for MM-VCEP
PP3
Not a missense variant, therefore, no REVEL score and SpliceAI is ≤0.50 (0.00) (BP4)
PP2
This rule is not applicable for MM-VCEP
Curation History
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