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Variant: NM_001754.5(RUNX1):c.900G>A (p.Thr300=)

CA10014272

561257 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 54ab3a88-8191-412c-8c7e-004ff6fe548b
Approved on: 2022-04-08
Published on: 2022-07-05

HGVS expressions

NM_001754.5:c.900G>A
NM_001754.5(RUNX1):c.900G>A (p.Thr300=)
NC_000021.9:g.34799368C>T
CM000683.2:g.34799368C>T
NC_000021.8:g.36171665C>T
CM000683.1:g.36171665C>T
NC_000021.7:g.35093535C>T
NG_011402.2:g.1190344G>A
ENST00000675419.1:c.900G>A
ENST00000300305.7:c.900G>A
ENST00000344691.8:c.819G>A
ENST00000399240.5:c.627G>A
ENST00000437180.5:c.900G>A
ENST00000482318.5:c.*490G>A
NM_001001890.2:c.819G>A
NM_001754.4:c.900G>A
NM_001001890.3:c.819G>A
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Likely Benign

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

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.900G>A (p.Thr300=) is a synonymous variant. Evolutionary conservation prediction algorithms predict the site as not being conserved (phyloP score -2.86554 ≤2.0) meeting BP7. This variant is a synonymous variant therefore no REVEL score is applicable and SpliceAI is ≤0.20 (0.00) (BP4). In summary, this variant meets the 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 score -2.86554 ≤2.0)
BP4
This variant is a synonymous variant therefore no REVEL score is applicable and SpliceAI is ≤0.20 (0.00) (BP4).
Not Met criteria codes
PS4
Case studies not found
PS2
Case studies not found
PS1
This amino acid has not been previously established as pathogenic
PS3
No functional studies found
BA1
Present in gnomAD v2 and v3 and does not meet criteria requirements.
PP1
No case studies found
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
Synonymous variant therefore not REVEl score and SpliceAI is not ≥0.38 (0.00)
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
Case studies not found
PM2
Present in gnomAD v2 and v3 and does not meet criteria requirements.
PM5
Not a missense varaint
PM1
Not a missense variant
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No an in-frame deletion/insertion
BS3
No functional studies found
BS4
No case studies found.
BS1
Present in gnomAD v2 and v3 and does not meet criteria requirements.
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No homozygotes present in gnomAD v2 and v3.
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
Not a null variant
Curation History
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