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The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_001754.4(RUNX1):c.882T>C (p.Pro294=)

CA10014276

532676 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 7c466984-fd0b-40c7-976c-85e8ccde732e
Approved on: 2022-07-07
Published on: 2022-07-07

HGVS expressions

NM_001754.4:c.882T>C
NM_001754.4(RUNX1):c.882T>C (p.Pro294=)
NC_000021.9:g.34799386A>G
CM000683.2:g.34799386A>G
NC_000021.8:g.36171683A>G
CM000683.1:g.36171683A>G
NC_000021.7:g.35093553A>G
NG_011402.2:g.1190326T>C
ENST00000675419.1:c.882T>C
ENST00000300305.7:c.882T>C
ENST00000344691.8:c.801T>C
ENST00000399240.5:c.609T>C
ENST00000437180.5:c.882T>C
ENST00000482318.5:c.*472T>C
NM_001001890.2:c.801T>C
NM_001001890.3:c.801T>C
NM_001754.5:c.882T>C
NM_001754.5(RUNX1):c.882T>C (p.Pro294=)
More

Likely Benign

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

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
This c.882T>C (p.Pro294=) synonymous variant is located at a non-conserved nucleotide per an evolutionary conservation prediction algorithm (PhyloP score = -0.178882 in GRCh38); it is not predicted to have any splicing impact per SpliceAI (BP7+BP4). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4 and BP7.
Met criteria codes
BP4
SpliceAI doesn't show any significant splicing impact (Δ scores ≤ 0.20).
BP7
Synonymous variant located at a non-conserved nucleotide (PhyloP = -0.178882 in GRCh38), and the variant is the reference nucleotide in one primate and/or 3 mammals. SpliceAI doesn't show any significant splicing impact.
Not Met criteria codes
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
gnomAD v2: ALL: 0.001988% (5/251482) - NFE: 0.002637% (3/113764) - AFR: 0.01231% (2/16250) gnomAD v3: ALL: 0.006570% (1/152216) - AMR: 0.006544% (1/15282)
PM3
Not applicable
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
MAF ≤ 0.15% gnomAD v2: ALL: 0.001988% (5/251482) - NFE: 0.002637% (3/113764) - AFR: 0.01231% (2/16250) gnomAD v3: ALL: 0.006570% (1/152216) - AMR: 0.006544% (1/15282)
BS2
Not applicable
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
MAF ≤ 0.015% gnomAD v2: ALL: 0.001988% (5/251482) - NFE: 0.002637% (3/113764) - AFR: 0.01231% (2/16250) gnomAD v3: ALL: 0.006570% (1/152216) - AMR: 0.006544% (1/15282)
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
Not applicable
BP1
Not applicable
BP5
Not applicable
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
Literature was not found in HGMD, Google/Google Scholar search, or COSMIC.
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Not applicable
PP3
SpliceAI doesn't show any significant splicing impact (Δ scores ≤ 0.20).
PP2
Not applicable
Curation History
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