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.351+3A>G

CA2580098625

2029145 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: aea1067a-896e-420f-a967-978dfcf98885

Approved on: 2024-08-01

Published on: 2024-08-01

HGVS expressions

NM_001754.5:c.351+3A>G

NM_001754.5(RUNX1):c.351+3A>G

NC_000021.9:g.34886840T>C

CM000683.2:g.34886840T>C

NC_000021.8:g.36259137T>C

CM000683.1:g.36259137T>C

NC_000021.7:g.35181007T>C

NG_011402.2:g.1102872A>G

ENST00000675419.1:c.351+3A>G

ENST00000300305.7:c.351+3A>G

ENST00000344691.8:c.270+3A>G

ENST00000358356.9:c.270+3A>G

ENST00000399237.6:c.315+3A>G

ENST00000399240.5:c.270+3A>G

ENST00000437180.5:c.351+3A>G

ENST00000455571.5:c.312+3A>G

ENST00000482318.5:c.59-6127A>G

NM_001001890.2:c.270+3A>G

NM_001122607.1:c.270+3A>G

NM_001754.4:c.351+3A>G

NM_001001890.3:c.270+3A>G

NM_001122607.2:c.270+3A>G

Uncertain Significance

BP4 PM2_Supporting

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

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.351+3A>G is an intronic variant which is completely absent from all population databases with at least 20x coverage for RUNX1 in gnomAD v2.1.1 and v3.1.2 (PM2_supporting). This intronic variant has a SpliceAI score ≤ 0.20 (0.02) (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: PM2_supporting, BP4.

BP4

This intronic variant has a SpliceAI score ≤ 0.20 (0.02) (BP4).

PM2_Supporting

This variant is completely absent from all population databases with at least 20x coverage for RUNX1 in gnomAD v2.1.1 and v3.1.2 (PM2_supporting).

BA1

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

PP4

This rule is not applicable to the MMVCEP.

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.

PM6

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

PM3

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

This is an intronic variant.

PM5

This is an intronic variant.

PVS1

This is an intronic variant.

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

BS2

This rule is not applicable to the MMVCEP.

BP5

This rule is not applicable to the MMVCEP.

BP7

phyloP score is > 2 and no change is reference nucleotide was seen in primate or mammal species.

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 to the MMVCEP.

BP1

This rule is not applicable to the MMVCEP.

PS2

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

PS4

Clinvar has one entry for this variant but the affected status is unknown. To our knowledge, no publication has reported this variant to date.

PS3

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

PS1

This is an intronic variant.

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