Variant classification summary

NM_001754.4:c.714C>A

RUNX1 · NP_001745.2:p.(Val238=) · NM_001754.4

GRCh37: chr21:36206798 G>T · GRCh38: chr21:34834501 G>T

Gene: RUNX1 Transcript: NM_001754.4

Final call

VUS

PM2 supporting PP3 supporting

Variant details

Gene

RUNX1

Transcript

NM_001754.4

Protein

NP_001745.2:p.(Val238=)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_001754.4:c.714C>A is a synonymous variant (p.Val238=) in exon 7 of RUNX1 that is absent from all population databases (gnomAD v2.1, v4.1).

2

SpliceAI predicts a strong cryptic splice donor gain (DS_DG=0.96), meeting the VCEP PP3 threshold of ≥0.38 for synonymous variants, suggesting a potential splicing impact.

3

PM2_Supporting is met: the variant is absent from gnomAD (MAF=0), meeting the VCEP threshold of ≤0.00005.

4

PVS1 is not met: this is a synonymous variant, not a null variant; predicted splicing effects without RNA confirmation route to PP3 under the RUNX1 VCEP.

5

PM1 is not met: codon 238 lies outside the Runt homology domain (AA 89-204), the critical functional domain specified by the VCEP.

6

No functional studies, de novo data, proband counts, co-segregation evidence, or literature reports are available for this variant.

7

Applying the point-based scoring system (Tavtigian 2020), PM2_Supporting contributes +1 point and PP3 contributes +1 point, for a total of 2 pathogenic points. The variant falls within the 0-5 point range and is classified as a Variant of Uncertain Significance (VUS).

Final determination: ClinGen Myeloid Malignancy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RUNX1 Version 3.1 v3.1 point-based framework yields a total score of 2, which maps to VUS under the specified Tavtigian-style ranges.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Not met	NM_001754.4:c.714C>A is a synonymous variant (p.Val238=) and does not fall into the PVS1 null-variant buckets (nonsense, frameshift, or canonical splice consensus). SpliceAI predicts a strong cryptic donor gain (DS_DG=0.96) but the RUNX1 VCEP routes predicted splicing effects to PP3 in the absence of RNA confirmation; PVS1 requires a null variant or RNA-proven splicing effect per the VCEP decision tree.	spliceai cspec
PS1	N/A	This variant is synonymous (p.Val238=) and produces no amino acid change; PS1 requires a same amino acid change as a previously established pathogenic variant.
PS2	Not met	No de novo occurrence data (with confirmed maternity and paternity) is available for this variant in the FPD/AML phenotype.
PS3	Not met	No in vitro or in vivo functional studies have been reported for this synonymous variant. No transactivation assay data or secondary functional assay data is available.
PS4	Not met	This variant has not been reported in any probands meeting RUNX1-phenotypic criteria. It is absent from ClinVar and no patient-level evidence is available.	clinvar
PS5	N/A	PS5 is not a recognized ACMG/AMP criterion. The standard pathogenic criteria are PVS1, PS1-PS4, PM1-PM6, and PP1-PP5.
PM1	Not met	This synonymous variant affects codon 238 (p.Val238=), which lies outside the RUNX1 Runt homology domain (RHD; AA 89-204). The VCEP PM1 rules require the variant to affect a residue within the RHD, with PM1_strong for the 13 hotspot residues and PM1_supporting for other AA 89-204.	cspec
PM2	Met	This variant is absent from gnomAD v2.1 and v4.1 across all populations, meeting the VCEP PM2_Supporting threshold (MAF ≤ 0.00005 with ≥2,000 alleles tested and ≥20x coverage).	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a missense change at an amino acid residue where a different pathogenic missense change has been previously observed. c.714C>A is a synonymous variant (p.Val238=) with no amino acid change; PM5 does not apply.
PM6	Not met	No assumed de novo occurrences have been reported for this variant in patients with FPD/AML phenotype.
PP1	Not met	No co-segregation data with disease in multiple affected family members is available for this variant.
PP2	N/A	PP2 is not applicable for RUNX1 per VCEP. The missense constraint z-score (2.08 in gnomAD) does not meet the SVI-recommended cutoff of ≥3.09, and nine benign/likely benign missense variants exist in ClinVar.
PP3	Met	This synonymous variant has a SpliceAI donor gain delta score of 0.96, which exceeds the VCEP PP3 threshold of ≥0.38 for synonymous variants, indicating creation of a cryptic novel splice donor site. This variant is not at a canonical splice site and no RNA confirmation data is available.	spliceai cspec
PP4	N/A	PP4 is not applicable for RUNX1 per VCEP. The FPD/AML phenotype is insufficiently specific and can be caused by multiple inherited predisposition syndromes, somatic mutations, or environmental factors.
PP5	N/A	PP5 is not for use per the ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation for this VCEP.
BA1	Not met	This variant is absent from gnomAD. The VCEP BA1 threshold requires MAF ≥ 0.0015 (0.15%) in any general continental population with ≥2,000 alleles and ≥5 variant alleles. MAF = 0 does not meet this threshold.	gnomad_v2 gnomad_v4
BS1	Not met	This variant is absent from gnomAD. The VCEP BS1 threshold requires MAF between 0.00015 (0.015%) and 0.0015 (0.15%) with ≥2,000 alleles and ≥5 variant alleles. MAF = 0 does not meet this threshold.	gnomad_v2 gnomad_v4
BS2	N/A	BS2 is not applicable for RUNX1 per VCEP. FPD/AML patients display incomplete penetrance, and the average age of onset of hematologic malignancies is 33 years.
BS3	Not met	No functional studies demonstrating normal transactivation (80-115% of wildtype) or normal function in secondary assays are available for this variant.
BS4	Not met	No segregation data is available to demonstrate lack of segregation in ≥2 informative meioses.
BP1	N/A	BP1 is not applicable for RUNX1 per VCEP, because both truncating and missense variants cause FPD/AML.
BP2	Not met	No evidence is available that this variant has been observed in trans with a known pathogenic variant or in cis with a pathogenic variant in any inheritance pattern.
BP4	Not met	The VCEP BP4 rule for synonymous variants requires SpliceAI ≤ 0.20. This variant has SpliceAI DS_DG = 0.96, which does not meet the BP4 threshold.	spliceai cspec
BP5	N/A	BP5 is not applicable per VCEP. Patients can carry two pathogenic variants in genes predisposing to hematologic malignancies.
BP6	N/A	BP6 is not for use per the ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation for this VCEP.
BP7	Not met	The VCEP BP7 rule for synonymous variants requires SpliceAI Δ scores ≤ 0.20 and exclusion from the last 3 nucleotides preceding a canonical donor splice site or first nucleotide following a canonical acceptor splice site. While c.714 is not in the terminal exon positions (exon 7 spans c.614-805), the SpliceAI DS_DG score of 0.96 exceeds the 0.20 threshold.	spliceai cspec

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