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.*2201T>G

CA320249723

897627 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 9357020a-2a29-4433-bc6c-057bf13f8800

Approved on: 2022-07-05

Published on: 2022-07-05

HGVS expressions

NM_001754.5:c.*2201T>G

NM_001754.5(RUNX1):c.*2201T>G

NC_000021.9:g.34789934A>C

CM000683.2:g.34789934A>C

NC_000021.8:g.36162231A>C

CM000683.1:g.36162231A>C

NC_000021.7:g.35084101A>C

NG_011402.2:g.1199778T>G

ENST00000675419.1:c.*2201T>G

ENST00000300305.7:c.*2201T>G

ENST00000344691.8:c.*2201T>G

ENST00000437180.5:c.*2201T>G

NM_001001890.2:c.*2201T>G

NM_001754.4:c.*2201T>G

NM_001001890.3:c.*2201T>G

Likely Benign

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"

BS1

PVS1 BA1 BS2 BS4 BS3 BP3 BP2 BP4 BP1 BP7 BP5 PS4 PS2 PS1 PS3 PP4 PP3 PP2 PP1 PM6 PM2 PM5 PM1 PM4 PM3

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.*2201T>G is a 3’UTR variant. This variant has a MAF of 0.0008115 (0.08115%, 12/14788 alleles) in the European (non-Finnish) subpopulation of the gnomAD v2 cohort is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). 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: BS1

BS1

MAF of 0.0008115 (0.08115%, 12/14788 alleles) in the European (non-finnish) subpopulation of the gnomAD v2 cohort is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1).

PVS1

3'UTR Variant

BA1

Meets BS1

BS2

This rule not applicable for MM-VCEP

BS4

No case study found

BS3

No studies found

BP3

This rule is not applicable for MM-VCEP

BP2

No case study found

BP4

3'UTR variant

BP1

This rule is not applicable for MM-VCEP

BP7

3'UTR Variant

BP5

This rule is not applicable for MM-VCEP

PS4

1 proband found in ClinVar without meeting RUNX1 phenotypic criteria

PS2

No case study found

PS1

3'UTR Variant

PS3

No studies found

PP4

This rule is not applicable for MM-VCEP

PP3

3'UTR variant

PP2

This rule is not applicable for MM-VCEP

PP1

No case study found

PM6

No case study found

PM2

meets BS1

PM5

3'UTR Variant

PM1

3'UTR Variant

PM4

3'UTR Variant

PM3

This rule is not applicable for MM-VCEP

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