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.613+1G>A

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA410207932

2023119 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 18ca2081-343f-481e-bf96-9dcb863a01f8

Approved on: 2025-01-15

Published on: 2025-01-15

HGVS expressions

NM_001754.5:c.613+1G>A

NM_001754.5(RUNX1):c.613+1G>A

NC_000021.9:g.34859473C>T

CM000683.2:g.34859473C>T

NC_000021.8:g.36231770C>T

CM000683.1:g.36231770C>T

NC_000021.7:g.35153640C>T

NG_011402.2:g.1130239G>A

ENST00000675419.1:c.613+1G>A

ENST00000300305.7:c.613+1G>A

ENST00000344691.8:c.532+1G>A

ENST00000358356.9:c.532+1G>A

ENST00000399237.6:c.577+1G>A

ENST00000399240.5:c.532+1G>A

ENST00000437180.5:c.613+1G>A

ENST00000467577.1:n.105+1G>A

ENST00000482318.5:c.*203+1G>A

NM_001001890.2:c.532+1G>A

NM_001122607.1:c.532+1G>A

NM_001754.4:c.613+1G>A

NM_001001890.3:c.532+1G>A

NM_001122607.2:c.532+1G>A

Uncertain Significance

PVS1_Strong PM2_Supporting

PM3 PM1 PM4 PM5 PM6 BA1 BS2 BS4 BS3 BS1 BP2 BP3 BP4 BP1 BP5 BP7 PS2 PS4 PS3 PS1 PP4 PP1 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.613+1G>A is a canonical splice site variant affecting the splice donor site at c.613 in intron 6, leading to exon 6 skipping. This results in an in-frame deletion of amino acids 171-205, including G170, within the Runt Homology Domain (RHD) (PVS1_strong). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting). 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: PVS1_strong, PM2_supporting.

PVS1_Strong

This variant affects the splice site c.613 in intron 6 leading to exon 6 skipping with In frame Δ171-205 and G170, deletion in RHD.

PM2_Supporting

This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2).

PM3

Not applicable.

PM1

Not applicable (splice variant).

PM4

Not applicable (splice variant).

PM5

Intronic variant.

PM6

nil data

BA1

PM2 met.

BS2

Not applicable.

BS4

nil data

BS3

nil data

BS1

PM2 met.

BP2

nil data

BP3

Not applicable.

BP4

PP3 met.

BP1

Not applicable.

BP5

Not applicable.

BP7

Not applicable (Splice variant).

PS2

nil data

PS4

nil data

PS3

nil data

PS1

Intronic variant.

PP4

Not applicable.

PP1

nil data

PP3

Not applicable (canonical splice site).

PP2

Not applicable.

Curation History

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