Classification rationale

PM2PP3 VUS

DNMT3A c.2322+3A>G

NM_022552.4:c.2322+3A>G in DNMT3A is an intronic variant at the +3 position of intron 19, outside the canonical ±1,2 splice consensus.¹ This variant is present at extremely low frequency in gnomAD v4.1 (AF = 6.82×10⁻⁶, grpmax FAF = 2.47×10⁻⁶, no homozygotes), meeting PM2 at supporting strength.² SpliceAI predicts a splice-altering effect with a max delta score of 0.64, meeting PP3 at supporting strength.³ This variant is absent from ClinVar and has not been reported in the medical literature; no experimental functional studies or segregation data are available.⁴ Based on the generic ACMG/AMP 2015 framework, the total evidence (PM2_supporting + PP3_supporting) is insufficient to classify this variant as likely pathogenic or pathogenic. The variant is classified as a Variant of Uncertain Significance (VUS).⁵

PM2 + PP3 → VUS

1 pvs1_variant_assessment

2 gnomad_v4 ↗

3 spliceai ↗

4 clinvar ↗

5 generic_acmg_combination_rules

Gene diagram · NM_022552.4 · variants mapped to exon structure

DNMT3A NM_022552.4

Fetching transcript structure from UCSC…

Applied criteria · 2 applied · 19 assessed

Applied · 2

Strength Supporting Moderate Strong Very strong

✓

PM2 supporting Pathogenic

This variant is present at extremely low frequency in population databases. In gnomAD v4.1, the allele frequency is 6.82×10⁻⁶ (11/1,614,020 alleles, no homozygotes) with a grpmax filtering allele frequency of 2.47×10⁻⁶, well below the 0.1% PM2 threshold. The highest subpopulation frequency is in the Finnish population at 3.12×10⁻⁵ (0.00312%).

gnomAD v4.1: AF = 6.82×10⁻⁶ (11/1614020)

gnomad_v2 ↗gnomad_v4 ↗

✓

PP3 supporting Pathogenic

SpliceAI predicts a splice-altering effect for this variant with a maximum delta score of 0.64, which exceeds the 0.5 threshold considered predictive of splicing impact. REVEL and BayesDel scores are not available as this is an intronic variant outside coding sequence.

SpliceAI max delta score = 0.64 (above 0.5 high-impact threshold)Variant is at intron 19 +3 positionwithin the splice donor region

spliceai ↗

Assessed · not applied

Pathogenic

PVS1 NM_022552.4:c.2322+3A>G is an intronic variant at the +3 position of intron 19, which is outside the canonical ±1,2 splice donor/acceptor consensus.

PS2 No de novo data are available for this variant.

PS3 No functional studies have been performed on this specific variant or a systematically characterized range that includes the c.2322+3 position.

PS4 No case-control data or statistical enrichment data are available for this variant.

PM1 This intronic variant at position c.2322+3 of intron 19 does not lie within a characterized protein functional domain (PWWP, ADD, or methyltransferase domains).

PM6 No de novo data are available for this variant.

PP1 No segregation data are available for this variant.

PP4 No specific phenotype or clinical data for the proband are available for review.

PP5 This variant is absent from ClinVar.

Benign

BA1 The variant allele frequency in gnomAD v4.1 (6.82×10⁻⁶) is far below the 1% BA1 threshold.

BS1 The variant allele frequency in gnomAD v4.1 (6.82×10⁻⁶) is far below the 0.3% BS1 threshold.

BS2 No evidence is available for homozygous occurrence in healthy individuals or observation in trans with a pathogenic variant in a fully penetrant dominant disorder.

BS3 No functional studies demonstrating a benign effect on protein function or splicing have been performed for this variant.

BS4 No segregation data demonstrating lack of cosegregation with disease are available.

BP2 No data are available for observation of this variant in trans with a pathogenic variant in a fully penetrant dominant disorder.

BP4 SpliceAI predicts a splice-altering effect (max delta = 0.64), which contradicts BP4.

BP5 No data are available demonstrating that this variant is observed in a case with an established alternate molecular basis for disease.

BP6 This variant is absent from ClinVar.

BP7 SpliceAI predicts a potential splice-altering effect (max delta = 0.64).

N/A · 7 PS1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3

Research & evidence

Population frequency

gnomAD v4.1

gnomAD v2.1

v4.1

This variant is present in gnomAD v4.1 (AF= 6.81528e-06; MAF= 0.00068%, 11/1614020 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 3.12383e-05; MAF= 0.00312%, 2/64024 alleles, homozygotes = 0); grpmax FAF= 2.47e-06.

v2.1

This variant is present in gnomAD v2.1 (AF= 3.97798e-06; MAF= 0.00040%, 1/251384 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89201e-05; MAF= 0.00289%, 1/34578 alleles, homozygotes = 0).

🇨🇦 CA

Absent from gnomAD-Canada v1.0.

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

0.00068% · 11 / 1,614,020
0 hom · FAF 0.00025%

European (Finnish) 2 / 64,024	0.0031%
Admixed American 1 / 59,998	0.0017%
Remaining individuals 1 / 62,484	0.0016%
European (non-Finnish) 7 / 1,179,988	0.00059%

+ 6 not observed (Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)

gnomAD v2.1

0.0004% · 1 / 251,384
0 hom

Admixed American

1 / 34,578

0.0029%

+ 7 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)

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 possible splice impact for this variant (max delta score = 0.64).

SpliceAI ↗

Functional No data

No calibrated functional assay or RNA evidence was identified for this variant.

OncoKB ↗

COSMIC

Somatic evidence

COSMIC

This variant has previously been reported in somatic cancers (COSMIC; COSV53040203, n = 1 times).

Hotspots

This variant does not lie in a statistically significant cancer hotspot.

COSMIC ↗

Sources & reference links

7Sources

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC