Back
LYFE SCIENCES
Project: HERA
NM_001001890.2:c.393T>C
p.Phe131=  ·  RUNX1
Starting
Initialising…
0%
Legacy Engine
Ready
View Legacy →
Classification rationale
1

The RUNX1 NM_001001890.2:c.393T>C (p.(Phe131=)) variant has been reported in ClinVar, where the ClinGen Myeloid Malignancy Variant Curation Expert Panel classified the equivalent RUNX1 transcript representation as uncertain significance and one clinical laboratory classified it as likely benign.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and is present at very low frequency in gnomAD v4.1 (1/1614108 alleles; AF 6.20e-07), with the highest observed subpopulation frequency of 1.67e-05 remaining below the RUNX1 PM2_Supporting threshold of 0.00005.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

Computational splicing prediction shows no significant splice impact, with a SpliceAI maximum delta score of 0.07, which supports BP4 and BP7 and does not meet the RUNX1 PP3 threshold.

spliceai ↗ cspec ↗
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
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1Absent from gnomAD v2.1.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 6.19537e-07; MAF= 0.00006%, 1/1614108 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66622e-05; MAF= 0.00167%, 1/60016 alleles, homozygotes = 0).
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Likely benign (1 clinical laboratory) and as Uncertain Significance by ClinGen Myeloid Malignancy Variant Curation Expert Panel (expert panel).
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55866238, n = 1 times).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueF131
Hotspots ↗