Variant classification summary

NM_001001890.2:c.624C>T

RUNX1 · NP_001001890.1:p.(Ala208=) · NM_001001890.2

GRCh37: chr21:36206807 G>A · GRCh38: chr21:34834510 G>A

Gene: RUNX1 Transcript: NM_001001890.2

Final call

VUS

PM2 supporting BP4 supporting benign BP6 supporting benign BP7 supporting benign

Variant details

Gene

RUNX1

Transcript

NM_001001890.2

Protein

NP_001001890.1:p.(Ala208=)

gnomAD AF

3.28514297190149e-05 (v4.1)

ClinVar

Likely Benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_001001890.2:c.624C>T (p.Ala208=) is a synonymous variant in exon 4 of RUNX1 that does not alter the amino acid sequence.

2

This variant is present at extremely low frequency in gnomAD (v4.1 grpmax FAF = 3.259e-05, 53/1,613,324 alleles), meeting PM2_Supporting under the MM-VCEP specification (MAF ≤0.00005).

3

SpliceAI predicts no splice impact (max delta = 0.02), meeting BP4 (SpliceAI ≤0.20 for synonymous variants) under the MM-VCEP specification.

4

The variant meets BP7 as a synonymous change not located in the critical splice region (not in the last 3 nucleotides of exon 4 nor the first nucleotide after the acceptor site), with SpliceAI ≤0.20.

5

The ClinGen Myeloid Malignancy VCEP classified this variant as Likely Benign (ClinVar ID 532686, SCV001366061, reviewed by expert panel), consistent with the computed Tavtigian score of -1 (PM2_Supporting +1, BP4 -1, BP7 -1).

6

No pathogenic evidence was identified: no de novo occurrences (PS2/PM6), no probands with FPD/AML phenotype (PS4), no functional data demonstrating damaging effect (PS3), no cosegregation data (PP1), the variant lies outside the RHD (PM1 not met), and in silico predictions do not support pathogenicity (PP3 not met).

7

Population frequencies are too low to meet BA1 (>0.15%) or BS1 (0.015%-0.15%), but the variant is not absent from population databases.

8

BS3 could not be independently assessed as the primary functional assay data reviewed by the expert panel is not publicly accessible through ClinVar; however, the expert panel's Likely Benign classification implies functional evidence was not supportive of pathogenicity.

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v3.1.0 point-based framework yields a total score of 1, 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	N/A	PVS1 is applicable only to null variants (nonsense, frameshift, canonical ±1,2 splice sites, initiation codon, exon deletion). NM_001001890.2:c.624C>T is a synonymous variant (p.Ala208=) that does not alter the amino acid sequence or create a null allele.
PS1	N/A	PS1 requires the same amino acid change as a previously established pathogenic variant. This is a synonymous variant that does not produce any amino acid change; there is no amino acid substitution to compare.
PS2	Not met	No proven de novo occurrences (with both maternity and paternity confirmed) of c.624C>T have been reported in patients with FPD/AML phenotype. The variant is observed in population databases at low frequency, consistent with inherited rather than de novo origin.	gnomad_v4
PS3	Not met	No well-established functional studies demonstrate a damaging effect for this variant. The ClinGen Myeloid Malignancy VCEP classified this variant as Likely Benign, which is inconsistent with PS3-level functional evidence of damage. No independently verifiable functional assay data showing altered transactivation or splicing for c.624C>T was identified.	clinvar
PS4	Not met	PS4 requires ≥4 probands meeting RUNX1-phenotypic criteria (OR 127.1) for Strong, 2-3 probands for Moderate, or 1 proband for Supporting. No probands with FPD/AML phenotype carrying c.624C>T have been reported in the literature or ClinVar submissions. The variant is observed in gnomAD at low frequency in presumably healthy population controls.	gnomad_v2 gnomad_v4 clinvar
PS5	N/A	PP5 is not for use under this VCEP as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
PM1	Not met	PM1 requires the variant to affect a residue within the Runt homology domain (RHD, AA 89-204). The variant is a synonymous change at codon 208 (Ala208=), which lies outside the RHD. Additionally, the variant does not alter the amino acid, so no residue is affected. PM1_strong applies only to 13 specific residues (R107, K110, A134, R162, R166, S167, R169, G170, K194, T196, D198, R201, R204), none of which are at position 208.	cspec
PM2	Met	PM2_Supporting is met under the MM-VCEP specification. The grpmax filtering allele frequency (FAF) in gnomAD v4.1 is 3.259e-05 (0.00326%), which is below the VCEP threshold of ≤0.00005 (0.005%). The variant is present in ≥2,000 alleles tested (1,613,324 total alleles).	gnomad_v4 cspec
PM5	N/A	PM5 requires a missense change at an amino acid residue where a different pathogenic missense change has been observed. This is a synonymous variant that does not alter the amino acid; there is no missense comparator to evaluate. PM5 is not applicable to synonymous variants.
PM6	Not met	PM6 requires ≥2 assumed de novo occurrences (PM6_Supporting) or ≥4 (PM6) in patients with FPD/AML phenotype, without confirmation of maternity and paternity. No assumed de novo occurrences of c.624C>T have been reported in the literature or ClinVar. The variant is observed in gnomAD population databases at low frequency, consistent with inherited transmission rather than de novo origin.	gnomad_v4 clinvar
PP1	Not met	PP1 requires ≥3 meioses (Supporting), 5-6 meioses (Moderate), or ≥7 meioses (Strong) of cosegregation with disease in affected families. No cosegregation data for c.624C>T with FPD/AML has been reported. The variant's presence in population databases at low frequency is not consistent with strong cosegregation with a rare autosomal dominant disorder.	gnomad_v4
PP2	N/A	PP2 is not applicable per the MM-VCEP. The RUNX1 missense constraint z-score (2.08-2.48) does not meet the SVI-recommended threshold of ≥3.09. Additionally, nine benign/likely benign missense variants exist in ClinVar for RUNX1. Furthermore, this variant is synonymous rather than missense.	cspec
PP3	Not met	PP3 for synonymous variants under the MM-VCEP requires SpliceAI ≥0.38, including the creation of cryptic novel splice sites. SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02), which is far below the 0.38 threshold. REVEL score is not available for this variant.	spliceai cspec
PP4	N/A	PP4 is not applicable per the MM-VCEP. The FPD/AML phenotype is rather unspecific and can be caused by other inherited predisposition syndromes, somatic mutations, or environmental factors, insufficient to meet the original ACMG/AMP PP4 rule.	cspec
PP5	N/A	PP5 is not for use under this VCEP as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	BA1 under the MM-VCEP specification requires a minor allele frequency ≥0.0015 (0.15%) in any general continental population dataset with ≥2,000 alleles tested and ≥5 variant alleles. The highest subpopulation frequency is in European (non-Finnish) at 0.00424% (gnomAD v4.1, 50/1,179,988 alleles), which is far below the 0.15% threshold. The gnomAD v2.1 NFE frequency is 0.00155%, also below 0.15%.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	BS1 under the MM-VCEP specification requires a minor allele frequency between 0.00015 (0.015%) and 0.0015 (0.15%) in any general continental population dataset with ≥2,000 alleles tested and ≥5 variant alleles. The highest subpopulation frequency is in European (non-Finnish) at 0.00424% (gnomAD v4.1), which is below the lower bound of 0.015%. The variant is too rare in all populations to meet BS1.	gnomad_v2 gnomad_v4 cspec
BS2	N/A	BS2 is not applicable per the MM-VCEP. FPD/AML patients display incomplete penetrance and the average age of onset of hematologic malignancies is 33 years, so observation in a healthy adult does not reliably exclude pathogenicity.	cspec
BS3	Not assessed	BS3 requires well-established functional studies (transactivation assays) showing no damaging effect. The ClinGen MM-VCEP classified this variant as Likely Benign, which implies functional data was reviewed and found to be non-damaging. However, the underlying functional assay data is not publicly accessible through the ClinVar submission record (SCV001366061, no validated PMIDs), and no independently verifiable published functional studies of c.624C>T were identified. BS3 cannot be independently adjudicated without access to the primary functional data reviewed by the expert panel.	clinvar
BS4	Not met	BS4 under the MM-VCEP specification requires observation in ≥2 informative meioses (genotype-negative, phenotype-positive family members). No such segregation data has been reported for c.624C>T. gnomAD reports 0 homozygotes for this variant across all datasets (v2.1 and v4.1), so homozygous observation in healthy individuals cannot support BS4.	gnomad_v2 gnomad_v4 cspec
BP1	N/A	BP1 is not applicable per the MM-VCEP. Both truncating and missense variants in RUNX1 cause FPD/AML, so a missense variant cannot be considered benign solely because truncating variants are the primary mechanism.	cspec
BP2	Not met	BP2 requires observation of the variant in trans with a known pathogenic variant in an individual without FPD/AML phenotype, or in cis with a pathogenic variant. No such observations have been reported. gnomAD shows 0 homozygotes across all datasets, so homozygous state evidence is unavailable.	gnomad_v2 gnomad_v4
BP4	Met	BP4 is met under the MM-VCEP specification for synonymous variants. The VCEP rule for synonymous variants requires SpliceAI ≤0.20. SpliceAI predicts no significant splice impact (max delta score = 0.02), which is well below the 0.20 threshold. Multiple lines of computational evidence suggest no impact on splicing.	spliceai cspec
BP5	N/A	BP5 is not applicable per the MM-VCEP. In rare circumstances, a patient can carry two pathogenic variants in genes predisposing to hematologic malignancies, so finding an alternate molecular basis does not reliably exclude RUNX1 pathogenicity.	cspec
BP6	Met	Expert panel ClinGen Myeloid Malignancy Variant Curation Expert Panel classified as Likely benign.	cspec clinvar
BP7	Met	BP7 is met under the MM-VCEP specification. The variant is a synonymous change (c.624C>T, p.Ala208=) located in exon 4, not within the last 3 nucleotides preceding the canonical donor splice site (c.722-724) or the first nucleotide following the canonical acceptor splice site (c.533). SpliceAI predicts no splice impact (max delta = 0.02 ≤ 0.20). Conservation data is no longer required per the VCEP v3.1.0 update.	spliceai cspec

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