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.177C>T (p.Gly59=)

CA320642905

739793 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 11f2a75d-86d1-42e3-bf2c-fe93b5285a49

HGVS expressions

NM_001754.5:c.177C>T

NM_001754.5(RUNX1):c.177C>T (p.Gly59=)

NC_000021.9:g.34887017G>A

CM000683.2:g.34887017G>A

NC_000021.8:g.36259314G>A

CM000683.1:g.36259314G>A

NC_000021.7:g.35181184G>A

NG_011402.2:g.1102695C>T

ENST00000675419.1:c.177C>T

ENST00000300305.7:c.177C>T

ENST00000344691.8:c.96C>T

ENST00000358356.9:c.96C>T

ENST00000399237.6:c.141C>T

ENST00000399240.5:c.96C>T

ENST00000437180.5:c.177C>T

ENST00000455571.5:c.138C>T

ENST00000482318.5:c.59-6304C>T

NM_001001890.2:c.96C>T

NM_001122607.1:c.96C>T

NM_001754.4:c.177C>T

NM_001001890.3:c.96C>T

NM_001122607.2:c.96C>T

Likely Benign

BP7 BP4

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

Evidence Links 0

Expert Panel

Myeloid Malignancy VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

NM_001754.5(RUNX1):c.177C>T (p.Gly59=) is a synonymous variant. Not REVEL score because synonymous variant and SpliceAI is ≤0.20 (0.00) meeting BP4. Evolutionary conservation prediction algorithms predict the site as not being conserved (phyloP 1.22672 < 2.0)meeting 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 and BP7.

BP7

Evolutionary conservation prediction algorithms predict the site as not being conserved (phyloP 1.22672 < 2.0)

BP4

Not REVEL score because synonymous variant and SpliceAI is ≤0.20 (0.00)

PS4

no case studies found

PS2

no case studies found

PS1

Amino acid has not been previously established as pathogenic

PS3

No functional studies found

PP1

No case studies found

PP4

This rule is not applicable for the MMVCEP

PP3

Not REVEL score because synonymous variant and SpliceAI is not ≥0.38 (0.00)

PP2

This rule is not applicable for the MMVCEP

PVS1

Not a null variant

BA1

Present in gnomAD v2 and v3 however does not meet code criteria.

BS4

No case studies found

BS3

No functional studies found

BS1

Present in gnomAD v2 and v3 however does not meet code criteria.

BS2

This rule is not applicable for the MMVCEP

PM5

Not a missense variant

PM1

Not a missense variant

PM3

This rule is not applicable for the MMVCEP

PM4

Not an in-frame deletion/insertion

PM6

no case studies found

PM2

Present in gnomAD v2 and v3 however does not meet code criteria.

BP5

This rule is not applicable for the MMVCEP

BP2

Present in gnomAD v2 and v3 however does not meet code criteria.

BP3

This rule is not applicable for the MMVCEP

BP1

This rule is not applicable for the MMVCEP

Approved on: 2022-07-05

Published on: 2022-07-05

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