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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  • 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.258G>C (p.Pro86=)

CA320642680

1153167 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: b4a61887-e91e-40b7-b1a3-f618a3b85aa1

HGVS expressions

NM_001754.5:c.258G>C
NM_001754.5(RUNX1):c.258G>C (p.Pro86=)
NC_000021.9:g.34886936C>G
CM000683.2:g.34886936C>G
NC_000021.8:g.36259233C>G
CM000683.1:g.36259233C>G
NC_000021.7:g.35181103C>G
NG_011402.2:g.1102776G>C
ENST00000675419.1:c.258G>C
ENST00000300305.7:c.258G>C
ENST00000344691.8:c.177G>C
ENST00000358356.9:c.177G>C
ENST00000399237.6:c.222G>C
ENST00000399240.5:c.177G>C
ENST00000437180.5:c.258G>C
ENST00000455571.5:c.219G>C
ENST00000482318.5:c.59-6223G>C
NM_001001890.2:c.177G>C
NM_001122607.1:c.177G>C
NM_001754.4:c.258G>C
NM_001001890.3:c.177G>C
NM_001122607.2:c.177G>C

Likely Benign

Met criteria codes 3
BP4 PM2_Supporting BP7
Not Met criteria codes 23
PS2 PS4 PS3 PS1 PM1 PM5 PM3 PM4 PM6 BA1 PVS1 BP1 BP2 BP3 BP5 BS2 BS4 BS3 BS1 PP1 PP3 PP2 PP4

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
Synonymous variant (no REVEL score applicable), and SpliceAI score is ≤ 0.20 (0.01) (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -3.228 (< 2.0)) (BP7). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting). 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, BP7, PM2_supporting.
Met criteria codes
BP4
Synonymous variant (no REVEL score applicable) and SpliceAI score is ≤0.20 (0.01) (BP4)
PM2_Supporting
This variant is completely absent from all population databases with at least 20x coverage for RUNX1
BP7
Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -3.228 (< 2.0))
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
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
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
This rule is not applicable for MM-VCEP
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
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
BP1
This rule is not applicable for MM-VCEP
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
This rule is not applicable for MM-VCEP
BP5
This rule is not applicable for MM-VCEP
BS2
This rule is not applicable for MM-VCEP
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
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
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
This rule is not applicable for MM-VCEP
PP4
This rule is not applicable for MM-VCEP
Approved on: 2024-06-24
Published on: 2024-06-24
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