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+19G>A

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA10014472

1639860 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 23f4917b-3e81-4d5d-8c33-3f1e8120d3bf

Approved on: 2025-01-15

Published on: 2025-01-15

HGVS expressions

NM_001754.5:c.613+19G>A

NM_001754.5(RUNX1):c.613+19G>A

NC_000021.9:g.34859455C>T

CM000683.2:g.34859455C>T

NC_000021.8:g.36231752C>T

CM000683.1:g.36231752C>T

NC_000021.7:g.35153622C>T

NG_011402.2:g.1130257G>A

ENST00000675419.1:c.613+19G>A

ENST00000300305.7:c.613+19G>A

ENST00000344691.8:c.532+19G>A

ENST00000358356.9:c.532+19G>A

ENST00000399237.6:c.577+19G>A

ENST00000399240.5:c.532+19G>A

ENST00000437180.5:c.613+19G>A

ENST00000467577.1:n.105+19G>A

ENST00000482318.5:c.*203+19G>A

NM_001001890.2:c.532+19G>A

NM_001122607.1:c.532+19G>A

NM_001754.4:c.613+19G>A

NM_001001890.3:c.532+19G>A

NM_001122607.2:c.532+19G>A

Likely Benign

BP4 BP7

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

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+19G>A is an intronic variant which meets criteria for likely benign classification. It has a SpliceAI score ≤ 0.20 (0.0) (BP4), and evolutionary conservation algorithms predict the site as not being conserved (PhyloP score ≤ 2.0 (0.49)) (BP7). 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.

BP4

This intronic variant has a SpliceAI score ≤ 0.20 (0.0) (BP4).

BP7

This variant has a SpliceAI score ≤ 0.20 (0.0) and evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score ≤ 2.0 (0.49)) (BP7).

PVS1

This is not a null variant.

BS2

not applicable

BS4

Segregation data for this variant has not been reported in literature.

BS3

In vitro or in vivo functional data has not been reported for this variant in the literature.

BS1

This variant does not have a MAF between 0.00015 (0.015%) and 0.0015 (0.15%) in any general continental dataset.

BP2

This variant has not been observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.

BP3

not applicable

BP1

not applicable

BP5

not applicable

PS2

De novo data for this variant has not been reported in literature.

PS4

Proband data for this variant has not been reported in literature.

PS3

In vitro or in vivo functional data has not been reported for this variant in the literature.

PS1

This variant is not a missense variant.

BA1

This variant does not have a MAF ≥ 0.0015 (0.15%) in any general continental population dataset.

PP4

not applicable

PP1

Segregation data for this variant has not been reported in literature.

PP3

This intronic variant does not have a SpliceAI score ≥ 0.38 (0.0).

PP2

not applicable

PM3

not applicable

PM1

This variant is not a missense variant.

PM4

This variant is not an in-frame deletion/insertion

PM5

This variant is not a missense variant.

PM6

De novo data for this variant has not been reported in literature.

PM2

This variant is present in at least one population database.

Curation History

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