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_001754.4(RUNX1):c.*2768A>C

CA10653554

339822 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 3689a40d-1e1d-45dc-8039-377d77f041f0

HGVS expressions

NM_001754.4:c.*2768A>C

NM_001754.4(RUNX1):c.*2768A>C

NC_000021.9:g.34789367T>G

CM000683.2:g.34789367T>G

NC_000021.8:g.36161664T>G

CM000683.1:g.36161664T>G

NC_000021.7:g.35083534T>G

NG_011402.2:g.1200345A>C

NM_001001890.2:c.*2768A>C

ENST00000300305.7:c.*2768A>C

ENST00000344691.8:c.*2768A>C

ENST00000437180.5:c.*2768A>C

Benign

BP2 BA1

PS1 PS3 PS4 BP7 BP4 PP3 PP1 PM5 PM1 PM4 PM2 PM6 PVS1 BS1 BS3 BS4

Evidence Links 0

Expert Panel

Myeloid Malignancy VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Myeloid Malignancy VCEP

The NM_001754.4(RUNX1):c.*2768A>C variant in the 3' UTR has an MAF of 0.0935 (9%, 3917/41896 alleles) in the African subpopulation of the gnomAD v3 cohort and is ≥ 0.0015 (0.15%) (BA1). This variant is detected in a homozygous state in 167 individuals in the gnomAD v3 population database (BP2). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2.

BP2

The variant is reported in 25 homozygotes in gnomAD v2.1.1 and 167 homozygotes in gnomAD v3 in the African population, meeting BP2

BA1

This 3' UTR variant is reported in gnomAD v2.1.1 at a frequency of 0.0964 (836/8672 alleles) and in gnomAD v3 at a frequency of 0.0935 (3917/41896 alleles) in the African population. It meets criteria for BA1.

PS1

N/A

PS3

No data currently available

PS4

The variant has not been reported in patients with familial platelet disorder with predisposition to hematologic malignancies in the literature, to the best of our knowledge.

BP7

N/A

BP4

N/A

PP3

N/A

PP1

No data currently available

PM5

N/A

PM1

N/A

PM4

N/A

PM2

Variant meets BA1

PM6

No data currently available

PVS1

N/A

BS1

Variant meets BA1

BS3

No data currently available

BS4

No data currently available

Approved on: 2020-01-13

Published on: 2020-01-14

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