Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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  • See Evidence submitted by expert panel for details.

Variant: NM_001754.4(RUNX1):c.54G>T (p.Met18Ile)

CA10014725

650319 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 63d601ee-e616-4441-84b5-ee21b4241765
Approved on: 2021-01-11
Published on: 2021-01-11

HGVS expressions

NM_001754.4:c.54G>T
NM_001754.4(RUNX1):c.54G>T (p.Met18Ile)
NC_000021.9:g.35048846C>A
CM000683.2:g.35048846C>A
NC_000021.8:g.36421143C>A
CM000683.1:g.36421143C>A
NC_000021.7:g.35343013C>A
NG_011402.2:g.940866G>T
ENST00000675419.1:c.54G>T
ENST00000300305.7:c.54G>T
ENST00000416754.1:c.54G>T
ENST00000437180.5:c.54G>T
ENST00000455571.5:c.54G>T
ENST00000475045.6:c.54G>T
ENST00000482318.5:c.54G>T
NM_001754.5:c.54G>T
NM_001754.5(RUNX1):c.54G>T (p.Met18Ile)
More

Likely Benign

Met criteria codes 1
BS1
Not Met criteria codes 25
PP1 PP2 PP3 PP4 PM6 PM2 PM1 PM3 PM5 PM4 BA1 BS2 BS4 BS3 BP4 BP3 BP1 BP2 PVS1 BP5 BP7 PS1 PS2 PS3 PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
The NM_001754.4:c.54G>T variant that results in a Met18Ile missense change has an MAF of 0.0002403 (0.02%, 6/24966 alleles) in the African subpopulation of the gnomAD v2.1.1 cohort, which is between 0.00015 (0.015%) and 0.0015 (0.15%) (BS1). This variant meets criteria to be classified as likely benign based on BS1 alone with no contradictory evidence supporting pathogenicity. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BS1.
Met criteria codes
BS1
The variant is reported at a frequency of 0.0002403 (6/24966 African alleles) in gnomAD v2.1.1 and at a frequency of 0.0001190 (5/42016 African alleles) in gnomAD v3. The frequency reported in gnomAD v2 meets criteria for BS1; threshold: >0.00015
Not Met criteria codes
PP1
No data currently available
PP2
MM-VCEP deemed N/A for RUNX1
PP3
The variant has a REVEL score of 0.256; does not meet threshold of >0.75
PP4
MM-VCEP deemed N/A for RUNX1
PM6
No data currently available
PM2
Meets BS1
PM1
N/A
PM3
MM-VCEP deemed N/A for RUNX1
PM5
No data currently available
PM4
N/A
BA1
Meets BS1
BS2
MM-VCEP deemed N/A for RUNX1
BS4
No data currently available
BS3
No data currently available
BP4
The variant has a REVEL score of 0.256; does not meet threshold of <0.15
BP3
MM-VCEP deemed N/A for RUNX1
BP1
MM-VCEP deemed N/A for RUNX1
BP2
N/A
PVS1
N/A
BP5
MM-VCEP deemed N/A for RUNX1
BP7
N/A
PS1
No data currently available
PS2
No data currently available
PS3
No data currently available
PS4
The variant has not been reported in the germ line of patients with familial platelet disorder with predisposition to hematologic malignancies in the literature, to the best of our knowledge.
Curation History
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