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.1152C>T (p.Pro384=)

CA512341268

3372635 (ClinVar)

Gene: RUNX1 (HGNC:861)

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome (MONDO:0011071)

Inheritance Mode: Autosomal dominant inheritance

UUID: 2ae4ad28-f5a9-4ca8-856d-109b9f1382ed

Approved on: 2025-03-26

Published on: 2025-03-26

HGVS expressions

NM_001754.5:c.1152C>T

NM_001754.5(RUNX1):c.1152C>T (p.Pro384=)

NC_000021.9:g.34792426G>A

CM000683.2:g.34792426G>A

NC_000021.8:g.36164723G>A

CM000683.1:g.36164723G>A

NC_000021.7:g.35086593G>A

NG_011402.2:g.1197286C>T

ENST00000675419.1:c.1152C>T

ENST00000300305.7:c.1152C>T

ENST00000344691.8:c.1071C>T

ENST00000399240.5:c.879C>T

ENST00000437180.5:c.1152C>T

ENST00000482318.5:c.*742C>T

NM_001001890.2:c.1071C>T

NM_001754.4:c.1152C>T

NM_001001890.3:c.1071C>T

Likely Benign

BP4 BP7

BA1 BS2 BS4 BS3 BS1 BP3 BP1 BP2 PVS1 BP5 PS2 PS4 PS3 PS1 PP1 PP3 PP2 PP4 PM1 PM4 PM5 PM3 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.1152C>T (p.Pro384=) is a synonymous variant which has a SpliceAI score ≤ 0.20 (0.00) and evolutionary conservation algorithms predict the site as not being conserved (PhyloP score ≤ 2.0 [1.06]) (BP4, 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 variant has a SpliceAI score ≤ 0.20 (0.00) (BP4).

BP7

This variant has a SpliceAI score ≤ 0.20 (0.00) and evolutionary conservation algorithms predict the site as not being conserved (PhyloP score ≤ 2.0 (1.06) (BP7).

BA1

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

BS2

This rule is not applicable for MM-VCEP

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.

BP3

This rule is not applicable for MM-VCEP

BP1

This rule is not applicable for MM-VCEP

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.

PVS1

This variant is not a null variant.

BP5

This rule is not applicable for MM-VCEP

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.

PP1

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

PP3

This variant does not have applicable in-silico data available.

PP2

This rule is not applicable for MM-VCEP

PP4

This rule is not applicable for MM-VCEP

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.

PM3

This rule is not applicable for MM-VCEP

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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