Variant: NM_001754.4(RUNX1):c.*2642A>G

CA10653555

339824 (ClinVar)

Gene: RUNX1

Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome

Inheritance Mode: Autosomal dominant inheritance

UUID: c614c417-4269-486f-95f6-e2c7edd76593

Approved on: 2020-05-13

Published on: 2020-06-02

HGVS expressions

NM_001754.4:c.*2642A>G
NM_001754.4(RUNX1):c.*2642A>G
NM_001001890.2:c.*2642A>G
NM_001001890.3:c.*2642A>G
ENST00000300305.7:c.*2642A>G
ENST00000344691.8:c.*2642A>G
ENST00000437180.5:c.*2642A>G
NC_000021.9:g.34789493T>C
CM000683.2:g.34789493T>C
NC_000021.8:g.36161790T>C
CM000683.1:g.36161790T>C
NC_000021.7:g.35083660T>C
NG_011402.2:g.1200219A>G

Benign

• Met criteria codes: BA1 BP2

• Not Met criteria codes: PVS1 BS1 BS3 BS4 BP4 BP7 PS1 PS3 PS4 PP3 PP1 PM2 PM6 PM5 PM4 PM1

Expert Panel

Myeloid Malignancy VCEP

Criteria Specification Information

Evidence submitted by expert panel

Myeloid Malignancy VCEP

The c.*2642A>G variant in the 3' UTR has an MAF of 0.01828 (1.8%, 282/15424 alleles) in the non-Finnish European subpopulation of the gnomAD v2.1.1 cohort and is ≥ 0.0015 (0.15%) (BA1). This variant is detected in a homozygous state in 9 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.

Met criteria codes

• BA1: The c.*2642A>G variant is reported at the highest MAF in the non-Finnish European population in gnomAD v2.1.1, at a frequency of 0.01828 (282/15424 alleles), with 3 homozygotes.
• BP2: A total of 3 and 9 homozygous individuals reported in gnomAD v2.1.1 and v3 , respectively.

Not Met criteria codes

• PVS1: N/A
• BS1: Variant meets BA1
• BS3: N/A
• BS4: N/A
• BP4: N/A
• BP7: N/A
• PS1: N/A
• PS3: N/A
• PS4: Variant meets BA1
• PP3: N/A
• PP1: N/A
• PM2: Variant meets BA1
• PM6: N/A
• PM5: N/A
• PM4: N/A
• PM1: N/A