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]

Link to SEPIO compliant JSON-LD document

Variant: NM_001754.5(RUNX1):c.205G>A (p.Gly69Ser)

CA320642805

948058 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: c696d202-7689-4459-8cdb-343cc71be655

HGVS expressions

NM_001754.5:c.205G>A

NM_001754.5(RUNX1):c.205G>A (p.Gly69Ser)

NC_000021.9:g.34886989C>T

CM000683.2:g.34886989C>T

NC_000021.8:g.36259286C>T

CM000683.1:g.36259286C>T

NC_000021.7:g.35181156C>T

NG_011402.2:g.1102723G>A

ENST00000675419.1:c.205G>A

ENST00000300305.7:c.205G>A

ENST00000344691.8:c.124G>A

ENST00000358356.9:c.124G>A

ENST00000399237.6:c.169G>A

ENST00000399240.5:c.124G>A

ENST00000437180.5:c.205G>A

ENST00000455571.5:c.166G>A

ENST00000482318.5:c.59-6276G>A

NM_001001890.2:c.124G>A

NM_001122607.1:c.124G>A

NM_001754.4:c.205G>A

NM_001001890.3:c.124G>A

NM_001122607.2:c.124G>A

Uncertain Significance

BP4

PS2 PS4 PS3 PS1 PP4 PP1 PP3 PP2 PM3 PM1 PM4 PM5 PM6 PM2 PVS1 BA1 BS2 BS4 BS3 BS1 BP2 BP3 BP1 BP5 BP7

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

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

NM_001754.5(RUNX1):c.205G>A (p.Gly69Ser) is a missense variant. The highest population minor allele frequency in gnomAD v3.1.2 is 0.0.00001470 (1/68046 alleles) in European (non-Finnish) population (PM2_Supporting, BS1, and BA1 not met). This missense variant has a REVEL score < 0.50 (0.439) and SpliceAI score is ≤ 0.20 (0) (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 missense variant has a REVEL score < 0.50 (0.439) and SpliceAI score is ≤ 0.20 (0) (BP4).

PS2

To our knowledge, no publication has reported this information to date.

PS4

Clinvar has one entry for this variant but there is no informations on phenotype. To our knowledge, no publication has reported this variant to date.

PS3

To our knowledge, this variant was not evaluated in transactivation assays.

PS1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PP4

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PP1

To our knowledge, no publication has reported this information to date.

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 to the MMVCEP.

PM3

This rule is not applicable to the MMVCEP.

PM1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PM4

This is a missense variant.

PM5

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PM6

To our knowledge, no publication has reported this information to date.

PM2

The highest population minor allele frequency in gnomAD v3.1.2 is 0.0.00001470 (1/68046 alleles) in European (non-Finnish) population (PM2_Supporting, BS1, and BA1 not met)

PVS1

This is a missense variant.

BA1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BS2

This rule is not applicable to the MMVCEP.

BS4

To our knowledge, no publication has reported this information to date.

BS3

To our knowledge, this variant was not evaluated in transactivation assays.

BS1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BP2

To our knowledge, no publication has reported this information to date.

BP3

This rule is not applicable to the MMVCEP.

BP1

This rule is not applicable to the MMVCEP.

BP5

This rule is not applicable to the MMVCEP.

BP7

This is not a synonymous variant.

Approved on: 2023-11-13

Published on: 2023-11-13

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