Evidence Repository - Clinical Genome Resources

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_001754.5(RUNX1):c.630A>G (p.Leu210=)

Curation Version - 1.1
Curation History
JSON LD for Version 1.1

CA10014389

464000 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 531a859a-dd57-4409-94fa-a7eb525c21d1

Approved on: 2025-03-26

Published on: 2025-03-26

HGVS expressions

NM_001754.5:c.630A>G

NM_001754.5(RUNX1):c.630A>G (p.Leu210=)

NC_000021.9:g.34834585T>C

CM000683.2:g.34834585T>C

NC_000021.8:g.36206882T>C

CM000683.1:g.36206882T>C

NC_000021.7:g.35128752T>C

NG_011402.2:g.1155127A>G

ENST00000675419.1:c.630A>G

ENST00000300305.7:c.630A>G

ENST00000344691.8:c.549A>G

ENST00000358356.9:c.549A>G

ENST00000399237.6:c.594A>G

ENST00000399240.5:c.532+24889A>G

ENST00000437180.5:c.630A>G

ENST00000469087.1:n.166A>G

ENST00000482318.5:c.*220A>G

NM_001001890.2:c.549A>G

NM_001122607.1:c.549A>G

NM_001754.4:c.630A>G

NM_001001890.3:c.549A>G

NM_001122607.2:c.549A>G

Uncertain Significance

BP4

PVS1 PM6 PM2 PM1 PM5 PM3 BS4 BS3 BS1 BS2 BP2 BP3 BP1 BP5 BP7 PS3 PS2 PS4 PS1 PP1 PP4 PP3 PP2

Evidence Links 0

Expert Panel

Myeloid Malignancy VCEP

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.630A>G (p.Leu210=) is a synonymous variant which has a SpliceAI score ≤ 0.20 (0.01) (BP4). In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4.

BP4

This synonymous variant does not have a SpliceAI score ≤ 0.20 (0.01).

PVS1

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

PM2

gnomAD v.4.1: 3/59890 alleles, MAF: 0.00005009 (0.00509%) in Admixed African subpopulation This variant is present in at least one population database.

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

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

gnomAD v.4.1: 3/59890 alleles, MAF: 0.00005009 (0.00509%) in Admixed African subpopulation This variant does not have a MAF between 0.00015 (0.015%) and 0.0015 (0.15%) in any general continental dataset.

BS2

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

BP1

This rule is not applicable for MM-VCEP

BP5

This rule is not applicable for MM-VCEP

BP7

This variant does not have a phyloP score < 2.0 (6.09).

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

No literature found in HGMD, Google+Google Scholar searches, or COSMIC by NM_001754 or NM_001001890.

PS1

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

This rule is not applicable for MM-VCEP

PP3

This synonymous variant does not have a SpliceAI score ≥ 0.38 (0.01)

PP2

This rule is not applicable for MM-VCEP

Curation History

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