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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Variant: NM_001754.5(RUNX1):c.1219_1221delinsGGGATCGTTCGGA (p.Tyr407fs)

CA2499225871

1065583 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 04603405-3e02-4884-8398-0105856dc8d2
Approved on: 2023-12-09
Published on: 2023-12-09

HGVS expressions

NM_001754.5:c.1219_1221delinsGGGATCGTTCGGA
NM_001754.5:c.1219_1221delTACinsGGGATCGTTCGGA
NM_001754.5(RUNX1):c.1219_1221delinsGGGATCGTTCGGA (p.Tyr407fs)
NC_000021.9:g.34792357_34792359delinsTCCGAACGATCCC
CM000683.2:g.34792357_34792359delinsTCCGAACGATCCC
NC_000021.8:g.36164654_36164656delinsTCCGAACGATCCC
CM000683.1:g.36164654_36164656delinsTCCGAACGATCCC
NC_000021.7:g.35086524_35086526delinsTCCGAACGATCCC
NG_011402.2:g.1197353_1197355delinsGGGATCGTTCGGA
ENST00000675419.1:c.1219_1221delinsGGGATCGTTCGGA
ENST00000300305.7:c.1219_1221delinsGGGATCGTTCGGA
ENST00000344691.8:c.1138_1140delinsGGGATCGTTCGGA
ENST00000399240.5:c.946_948delinsGGGATCGTTCGGA
ENST00000437180.5:c.1219_1221delinsGGGATCGTTCGGA
ENST00000482318.5:c.*809_*811delinsGGGATCGTTCGGA
NM_001001890.2:c.1138_1140delinsGGGATCGTTCGGA
NM_001754.4:c.1219_1221delinsGGGATCGTTCGGA
NM_001001890.3:c.1138_1140delinsGGGATCGTTCGGA
More

Likely Pathogenic

Met criteria codes 3
PM2_Supporting PM5_Supporting PVS1_Strong
Not Met criteria codes 23
BP5 BP7 BP4 BP3 BP1 BP2 PS1 PS2 PS3 PS4 BA1 PP1 PP2 PP3 PP4 PM1 PM3 PM4 PM6 BS1 BS4 BS3 BS2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
The c.1219_1221delinsGGGATCGTTCGGA (p.Tyr407Glyfs*196) (NM_001754.5) variant in RUNX1 - whose mechanism of disease is established to be loss-of-function - is a protein extension variant that is predicted to escape nonsense-mediated decay but alters a region critical to protein function (transactivation domain, inhibitory domain, and/or the VWRPY motif) (PVS1_Strong). This variant is absent from gnomAD v2, v3, and v4 with at least 20 coverage (PM2_Supporting). Only the somatic variant has been reported in a patient with mixed phenotype acute leukemia (ClinVar SCV001573164.1), but it is of note that other pathogenic/likely pathogenic frameshift alterations in exon 8 have been reported (PMID: 35764482), and other C-terminal frameshift variants have shown loss of transactivation ability and a dominant-negative effect (PMID: 14615365, 19808697, 25840971) (PM5_Supporting). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant hereditary thrombocytopenia and hematologic cancer predisposition syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy VCEP: PVS1_Strong, PM2_Supporting, and PM5_Supporting. (Version 2; date of approval)
Met criteria codes
PM2_Supporting
Completely absent from gnomAD v2+v3+v4 with a mean coverage of at least 20X.
PM5_Supporting
Other pathogenic or likely pathogenic frameshift alterations in exon 8 have been reported (Feurstein et al., 2022, 35764482 - Supplementary Table 5).
PVS1_Strong
Fig. 2 in PMID: 31648317
Not Met criteria codes
BP5
Not applicable
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
Not applicable
BP1
Not applicable
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
PS3
No literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
PS4
The variant was confirmed somatically in a patient with mixed phenotype acute leukemia (ClinVar SCV001573164.1). No additional cases were found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
BA1
Completely absent from gnomAD v2+v3+v4 with a mean coverage of at least 20X.
PP1
No literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
PP2
Not applicable
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Not applicable
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
Not applicable
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
BS1
Completely absent from gnomAD v2+v3+v4 with a mean coverage of at least 20X.
BS4
No literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
BS3
No literature was found in LOVD, HGMD, ClinVar, COSMIC, Mastermind, and Google/Google Scholar searches.
BS2
Not applicable
Curation History
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