Classification rationale

PVS1PM2PM5 Pathogenic

RUNX1 c.707dup frameshift · exon 7

PVS1 (Very Strong): out-of-frame frameshift (p.Met236IlefsTer25) predicted to trigger nonsense-mediated decay, an established RUNX1 disease mechanism. PM2 (Supporting): variant absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with MAF 0 versus the <=0.00005 threshold. PM5 (Supporting): frameshift downstream of c.98 with no splicing impact (SpliceAI max delta 0.036, <=0.20). These criteria total 10 points (PVS1 very strong, PM2 and PM5 supporting), meeting Rule 1 (>=10) and classifying the variant as Pathogenic.

PVS1 + PM2 + PM5 → Pathogenic

Gene diagram · NM_001754.4 · variants mapped to exon structure

RUNX1 NM_001754.4

Fetching transcript structure from UCSC…

Applied criteria · 3 applied · 12 assessed

Applied · 3

Strength Supporting Moderate Strong Very strong

✓

PVS1 very strong Pathogenic

Met (Very Strong): out-of-frame duplication creates a premature stop codon predicted to trigger nonsense-mediated decay, the established RUNX1 loss-of-function mechanism.

Mutalyzer/VariantValidator normalization (prefetch.json) confirms NM_001754.4:c.707dupT as a duplication of T at c.707 with predicted protein NP_001745.2:p.(Met236IlefsTer25); wild-type protein length 481 aa, predicted mutant length 260 aa, frameshift start at position 235.VariantValidator places the variant in exon 7 of NM_001754.4 (start_exon/end_exon = 7) for GRCh37, GRCh38 and NG_011402.2; exon 7 spans c.614-805, so c.707 is internal to the exon and not near a splice junction.The ClinGen Myeloid Malignancy VCEP RUNX1 v3.1 (cspec, doc 135637580) designates NM_001754.4 (RUNX1c) as the default transcript and states that RUNX1 LOF variants are a common mechanism of disease in FPD/AML; PVS1 is applied per a modified RUNX1 PVS1 decision tree, with C-terminal truncating variants not predicted to undergo NMD classified as PVS1_strong and exon 1-3 deletions (presumably affecting only isoform c) as PVS1_moderate.

cspec ↗pvs1_generic_framework ↗spliceai ↗

✓

PM2 supporting Pathogenic

Met (Supporting): absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with MAF 0 versus the <=0.00005 threshold.

MM-VCEP RUNX1 v3.1 PM2 rule (cspec): 'PM2_Supporting: Minor allele frequency ≤ 0.00005 with at least 2000 alleles tested around and 20x coverage at the position'; caveat: evaluate using the GrpMax FAF when available in gnomAD v4.1.0, otherwise require all subpopulations to meet the threshold; the mean coverage of RUNX1 in the population database used should be at least 20x.Variant absent from gnomAD v2.1 (exome, GRCh37; 21-36206804-C-CA), gnomAD v4.1 (joint exome+genome, GRCh38; chr21-34834507-C-CA), and gnomAD-Canada v1.0 (genomes; 21-34834507-C-CA): MAF = 0 in every dataset and every continental subpopulation, satisfying the <= 0.00005 threshold; each dataset contains far more than the required 2,000 alleles (gnomAD v2.1 exomes alone exceed 250,000 alleles).Ancestry consideration: no continental population shows any allele at this position, so the 'all subpopulations meet the threshold' fallback of the VCEP caveat is satisfied and no ancestry-specific excess exists.

cspec ↗gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

✓

PM5 supporting review Pathogenic

Met (Supporting): frameshift downstream of c.98 with SpliceAI max delta 0.036 (<=0.20), indicating no splicing impact.

MM-VCEP v3.1 (CSPEC doc 135637580) PM5_Supporting rule text: 'PM5_Supporting is also applied to nonsense/frameshift variants that are downstream of c.98 (in transcript NM_001754.4)', with caveats that the variant must not impact splicing (RNA assay or SpliceAI <= 0.20) and that PM5 cannot be used if PM1 was applied at any strength level.SpliceAI lookup for NM_001754.4:c.707dup (variant 21-36206804-C-CA): max delta score = 0.036 (DS_AL 0.036, DS_DG 0.031, DS_DL 0.027, DS_AG 0.002), i.e. <= 0.20; no significant splice impact predicted.pm5_candidates.json confirms the variant consequence class is frameshift (not missense), so classic same-residue missense PM5 search was flagged not applicable; consistent with applying the VCEP's explicit frameshift-downstream-of-c.98 extension instead.

cspec ↗spliceai ↗

Assessed · not applied

Pathogenic

PS2 Not assessed: no proband genotype, parental testing, or family history data were available for this variant.

PS3 Not assessed: no variant-specific functional assay data (transactivation or secondary assays) were available.

PS4 Not assessed: no proband observations were found in ClinVar, gnomAD, COSMIC, or the reviewed literature.

PM1 Not met: p.Met236 lies outside the Runt Homology Domain (amino acids 89-204) to which PM1 is restricted.

PM6 Not assessed: no assumed de novo occurrences were reported; no parental testing data or ClinVar submissions exist.

PP1 Not assessed: no pedigree or segregation data were available for this variant.

PP3 Not met: SpliceAI max delta 0.036 versus the >=0.38 threshold; no calibrated predictor scores support pathogenicity.

Benign

BA1 Not met: absent from all gnomAD datasets, with MAF 0 versus the >=0.0015 stand-alone threshold.

BS1 Not met: MAF 0 is below the 0.00015 lower bound of the BS1 range.

BS3 Not assessed: no functional studies demonstrating normal transactivation or function were available.

BS4 Not assessed: no informative meioses showing lack of segregation were reported.

BP2 Not met: no trans, cis, or homozygous observations of the variant were found.

N/A · 13 PS1 · PM3 · PM4 · PP2 · PP4 · PP5 · BS2 · BP1 · BP3 · BP4 · BP5 · BP6 · BP7

Research & evidence

Population frequency · supports pathogenic

gnomAD v4.1

gnomAD v2.1

v4.1

Absent from gnomAD v4.1.

v2.1

Absent from gnomAD v2.1.

🇨🇦 CA

Absent from gnomAD-Canada v1.0.

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v2.1

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD Canada 🇨🇦

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant is absent from ClinVar.

ClinVar ↗

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04).

SpliceAI ↗

Functional 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 ↗

COSMIC

Cancer hotspots

Somatic evidence Not in COSMIC / hotspots

COSMIC

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Hotspots

This variant does not lie in a statistically significant hotspot.

COSMIC ↗ Hotspots ↗

Sources & reference links

9Sources

CSpec VCEP

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots

Triaged references · 3 PMIDs not cited in assessment

15386419 ↗ Frequent downregulation of the runt domain transcription factors RUNX1, RUNX3 and their cofactor CBFB in gastric cancer. ONCOKB

15864279 ↗ The RUNX genes: gain or loss of function in cancer. ONCOKB

17394134 ↗ Fusion gene-mediated truncation of RUNX1 as a potential mechanism underlying disease progression in the 8p11 myeloproliferative syndrome. ONCOKB