Classification rationale

PM2 VUS

EZH2 c.1966G>A

NM_004456.4:c.1966G>A (p.Ala656Thr) is a missense variant in EZH2 that is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).¹ No additional pathogenic or benign criteria are met. The variant has not been reported in ClinVar, has no functional studies, no segregation data, no de novo observations, and in silico predictors are discordant (REVEL 0.753 damaging; BayesDel 0.311 benign).² With a single supporting criterion (PM2) and no conflicting benign evidence, the variant is classified as a Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 guidelines (PMID:25741868).³

PM2 → VUS

1 gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

2 clinvar ↗revelbayesdelspliceai ↗

3 generic_acmg_combination_rules

Gene diagram · NM_004456.4 · variants mapped to exon structure

EZH2 NM_004456.4

Fetching transcript structure from UCSC…

Applied criteria · 1 applied · 21 assessed

Applied · 1

Strength Supporting Moderate Strong Very strong

✓

PM2 supporting Pathogenic

The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with an allele frequency of 0. This meets the PM2 threshold for absence from population databases (allele frequency <0.1% for non-VCEP).

Absent from gnomAD v2.1 (AF=0)Absent from gnomAD v4.1 (AF=0)Absent from gnomAD-Canada v1.0 (AF=0)

gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

Assessed · not applied

Pathogenic

PS1 No prior report of a different nucleotide change at codon 656 resulting in the same p.Ala656Thr missense alteration with a pathogenic classification.

PS2 No de novo observation has been reported for this variant.

PS3 No well-established functional studies demonstrating a damaging effect have been reported for this variant.

PS4 No case-control studies or statistical evidence of enrichment in affected individuals versus controls.

PM1 The variant does not lie in a statistically significant mutational hotspot as assessed by Cancer Hotspots.

PM6 No de novo observation has been reported for this variant.

PP1 No co-segregation data are available for this variant.

PP2 HCI prior score is unavailable for EZH2 (gene not supported by the HCI prior database).

PP3 Insufficient consensus among multiple in silico predictors.

PP4 No clinical phenotype or family history data are available to assess whether the patient's presentation is highly specific for EZH2-associated Weaver syndrome.

PP5 No reputable source has classified this variant as pathogenic.

Benign

BA1 The variant is absent from gnomAD (allele frequency = 0).

BS1 The variant is absent from gnomAD (allele frequency = 0).

BS2 The variant has not been observed in any healthy adult individuals in population databases.

BS3 No well-established functional studies demonstrating no deleterious effect have been reported for this variant.

BS4 No segregation data are available to assess lack of segregation with disease in affected families.

BP1 EZH2 Weaver syndrome is primarily caused by missense variants through a dominant-negative mechanism, not by truncating mutations.

BP2 No observation of this variant in trans with a known pathogenic dominant variant in EZH2.

BP4 Insufficient consensus among multiple in silico predictors for a benign effect.

BP5 No case has been reported in which this variant is found in an individual with an alternate molecular basis for disease.

BP6 No reputable source has classified this variant as benign.

N/A · 3 PVS1 · PM5 · BP7

Research & evidence

Population frequency

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 = 0.02). REVEL score = 0.753. BayesDel score = 0.311152.

SpliceAI ↗

Functional Unknown Oncogenic Effect

OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. EZH2, an epigenetic modifier, is altered by mutation and/or overexpression in solid tumors and hematologic malignancies.

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

8Sources

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots

Re-run this variant?