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]
  • Gene obtained from curated document aligns with ClinVar but not with the Allele Registry data
  • 'cspec' property is found but contains no ID!
  • See Evidence submitted by expert panel for details.

Variant: NM_001754.5(RUNX1):c.1412_1413del (p.Arg471fs)

1349747 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: ef910371-30e0-4df3-b6ee-2bfab0c3766d
Approved on: 2023-12-09
Published on: 2023-12-09

HGVS expressions

NM_001754.5:c.1412_1413del
NM_001754.5(RUNX1):c.1412_1413del (p.Arg471fs)

Likely Pathogenic

Met criteria codes 3
PVS1_Strong PM2_Supporting PM5_Supporting
Not Met criteria codes 22
PM6 PM1 PM4 PM3 BA1 BS4 BS3 BS1 BS2 BP5 BP7 BP3 BP2 BP4 BP1 PS2 PS1 PS3 PP4 PP1 PP3 PP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
NM_001754.5(RUNX1):c.1412_1413del (p.Arg471fs) is a frameshift variant that is not predicted to undergo NMD. (PVS1_strong, CNV tree). This variant is completely absent from all population databases (PM2_supporting). This variant is a nonsense/frameshift variant that is downstream of c.98 (PM5_Supporting). In summary, this variant meets criteria to be classified as likely pathogenic. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: PVS1_strong, PM2_supporting, PM5_supporting.
Met criteria codes
PVS1_Strong
NM_001754.5(RUNX1):c.1412_1413del (p.Arg471fs) is a frameshift variant that is not predicted to undergo NMD. (PVS1_strong, CNV tree)
PM2_Supporting
This variant is completely absent from all population databases
PM5_Supporting
This variant is a nonsense/frameshift variant that is downstream of c.98 (PM5_Supporting).
Not Met criteria codes
PM6
De novo data for this variant has not been reported in literature.
PM1
This variant is not a missense variant.
PM4
This variant is not an in-frame deletion/insertion.
PM3
This rule is not applicable for MM-VCEP.
BA1
This variant is completely absent from all population databases
BS4
No case studies found
BS3
No functional studies found
BS1
This variant is completely absent from all population databases
BS2
This rule is not applicable for MM-VCEP.
BP5
This rule is not applicable for MM-VCEP.
BP7
Not a synonymous or intronic variant
BP3
This rule is not applicable for MM-VCEP.
BP2
No homozygotes present in gnomAD v2.1.1 or v3.1.2
BP4
Not a missense, synonymous, or intronic variant.
BP1
This rule is not applicable for MM-VCEP.
PS2
De novo data for this variant has not been reported in literature.
PS1
There has not yet been a missense change determined to be pathogenic at this amino acid residue.
PS3
No functional studies found
PP4
This rule is not applicable for MM-VCEP.
PP1
No case studies found
PP3
Not a missense, synonymous, or intronic variant
PP2
This rule is not applicable for MM-VCEP.
Curation History
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