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]
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Variant: NM_001754.5(RUNX1):c.558C>T (p.Val186=)

CA320618002

532684 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 2b439f5e-095f-43db-b2a0-fa5a888f997b
Approved on: 2022-02-10
Published on: 2022-07-05

HGVS expressions

NM_001754.5:c.558C>T
NM_001754.5(RUNX1):c.558C>T (p.Val186=)
NC_000021.9:g.34859529G>A
CM000683.2:g.34859529G>A
NC_000021.8:g.36231826G>A
CM000683.1:g.36231826G>A
NC_000021.7:g.35153696G>A
NG_011402.2:g.1130183C>T
ENST00000675419.1:c.558C>T
ENST00000300305.7:c.558C>T
ENST00000344691.8:c.477C>T
ENST00000358356.9:c.477C>T
ENST00000399237.6:c.522C>T
ENST00000399240.5:c.477C>T
ENST00000437180.5:c.558C>T
ENST00000467577.1:n.50C>T
ENST00000482318.5:c.*148C>T
NM_001001890.2:c.477C>T
NM_001122607.1:c.477C>T
NM_001754.4:c.558C>T
NM_001001890.3:c.477C>T
NM_001122607.2:c.477C>T

Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 24
BP5 BP2 BP3 BP1 PS4 PS2 PS3 PS1 PP1 PP4 PP3 PP2 PM6 PM2 PM5 PM1 PM3 PM4 PVS1 BA1 BS4 BS3 BS1 BS2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
NM_001754.5(RUNX1):c.558C>T (p.Val186=) is synonymous variant. No REVEL score because synonymous variant and SpliceAI is ≤0.20 (0.00) meeting BP4 . Evolutionary conservation prediction algorithms predict the site as not being conserved (phyloP -1.3873 < 2.0) meeting BP7. 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: BP4 and BP7
Met criteria codes
BP7
Evolutionary conservation prediction algorithms predict the site as not being conserved (phyloP -1.3873 < 2.0)
BP4
No REVEL score because synonymous variant and SpliceAI is ≤0.20 (0.00)
Not Met criteria codes
BP5
This rule is not applicable for the MMVCEP
BP2
No homozygotes found in v2 and v3 gnomAD
BP3
This rule is not applicable for the MMVCEP
BP1
This rule is not applicable for the MMVCEP
PS4
No case studies found
PS2
No case studies found
PS3
No functional studies found. Present in COSMIC (COSM9800149)
PS1
Amino acid change not established as pathogenic
PP1
No case studies found
PP4
This rule is not applicable for the MMVCEP
PP3
No REVEL score because synonymous variant and SpliceAI is not ≥0.38 (0.00)
PP2
This rule is not applicable for the MMVCEP
PM6
No case studies found
PM2
Absent in v2 but present in v3 however does not meet criteria requirements
PM5
Not a missense variant
PM1
Not a missense variant
PM3
This rule is not applicable for the MMVCEP
PM4
Not an in-frame deletion/insertion
PVS1
Not a null variant
BA1
Absent in v2 but present in v3 however does not meet criteria requirements
BS4
No case studies found
BS3
No functional studies found. Present in COSMIC (COSM9800149)
BS1
Absent in v2 but present in v3 however does not meet criteria requirements
BS2
This rule is not applicable for the MMVCEP
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