Back
LYFE SCIENCES
Project: HERA
NM_001001890.2:c.319_323del
p.Ala107GlnfsTer2  ·  RUNX1
Starting
Initialising…
0%
Legacy Engine
Ready
View Legacy →
Classification rationale
1

The RUNX1 c.319_323del (p.Ala107GlnfsTer2; p.A107Qfs*2) variant has been reported in ClinVar and classified as Pathogenic by the ClinGen Myeloid Malignancy Variant Curation Expert Panel.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, which is below the RUNX1 PM2_Supporting threshold of <=0.00005 and far below the BS1 and BA1 population thresholds.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

This 5-bp deletion causes an early frameshift with a premature stop codon, and the exact expert-panel ClinVar record states that the default RUNX1 transcript consequence p.Ala134fs is predicted to undergo nonsense-mediated decay, supporting PVS1; the same record also applied RUNX1-specific PM5_Supporting because the frameshift is downstream of c.98.

clinvar ↗ cspec ↗
4

SpliceAI predicts no significant splice impact for this variant (max delta score 0.03), which is below the RUNX1 PP3 threshold of 0.38 and consistent with the <=0.20 splice caveat used for PM5_Supporting.

spliceai ↗ cspec ↗ clinvar ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
—
—
Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
—
Research and evidence
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory) and as Pathogenic by ClinGen Myeloid Malignancy Variant Curation Expert Panel (expert panel).
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueA107
Hotspots ↗