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EZH2
Final classification
Likely Benign
EZH2 c.1852-9A>C · p.?
EZH2

NM_004456.4:c.1852-9A>C is an intronic variant in EZH2 located 9 bases upstream of exon 15, outside canonical splice consensus sites.

Gene
EZH2
Transcript
NM_004456.4
HGVS · transcript:coding
NM_004456.4:c.1852-9A>C
Consequence
N/A
GRCh38
chr7:148811729 T>G
GRCh37
chr7:148508821 T>G
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign, BP6 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign, BP6 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP4BP6 Likely Benign
EZH2 c.1852-9A>C

NM_004456.4:c.1852-9A>C is an intronic variant in EZH2 located 9 bases upstream of exon 15, outside canonical splice consensus sites.1 This variant is present in gnomAD at very low frequency (v2.1: 11/246,568 alleles, AF=0.0045%; v4.1: 73/1,608,258 alleles, AF=0.0045%) with no homozygotes observed. The allele frequency falls well below the 0.1% PM2 threshold (PM2_supporting).2 SpliceAI predicts no significant splice impact (max delta score = 0.02), providing computational evidence that the variant does not disrupt normal splicing (BP4_supporting).3 ClinVar classifies this variant as Likely benign (VariationID 416828) based on a submission from Labcorp Genetics with ACMG criteria provided. This constitutes supporting benign evidence from a reputable clinical source (BP6_supporting).4 PVS1 is not applicable as the variant lies outside canonical splice ±1,2 consensus sites and does not fall into null-variant buckets per ClinGen SVI recommendations (PMC6185798). PM5, PP2, BP1, BP7 are not applicable as the variant is intronic, not missense or synonymous. BP3, PM3, PM4 were skipped per instruction as trivially not applicable.5 Applying generic ACMG/AMP 2015 final classification combination rules: two supporting benign criteria (BP4, BP6) are met, which reaches the threshold for Likely benign. One supporting pathogenic criterion (PM2) is also met but does not alter the Likely benign classification under the standard combination rules.6

PM2 + BP4 + BP6 Likely Benign
Gene diagram · NM_004456.4 · variants mapped to exon structure
EZH2 NM_004456.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 16 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is present in gnomAD at very low frequency (v2.1: AF=4.46e-05, 11/246,568 alleles; v4.1: AF=4.54e-05, 73/1,608,258 alleles; grpmax FAF=5.41e-05). The allele frequency is well below the 0.1% threshold for PM2 in non-VCEP adjudication.
gnomAD v2.1 AF=0.0045% (11/246568)v4.1 AF=0.0045% (73/1
BP4 supporting Benign
SpliceAI predicts no significant splice impact for this intronic variant (max delta score = 0.02), providing computational evidence that the variant does not disrupt normal splicing.
SpliceAI max delta=0.02no predicted donor gaindonor loss
BP6 supporting Benign
This variant has been classified as Likely benign by Labcorp Genetics (formerly Invitae), a reputable clinical diagnostic laboratory, with ACMG criteria provided (ClinVar VariationID: 416828, SCV000562813).
ClinVar Likely benign classification from Labcorp Genetics (criteria providedsingle submitter).
Assessed · not applied
Pathogenic
PS2 No de novo observation for NM_004456.4:c.1852-9A>C was identified in the reviewed literature or ClinVar submissions.
PS3 No well-established functional studies evaluating the impact of this intronic variant on splicing or protein function were identified.
PS4 The variant has been observed in ClinVar as Likely benign (single submitter) and is present in gnomAD at low frequency (AF ~0.0045%).
PM1 The variant is not located in a well-established mutational hotspot or critical functional domain.
PM6 No de novo observation (with or without maternity/paternity confirmation) for NM_004456.4:c.1852-9A>C was identified in the reviewed literature.
PP1 No cosegregation data available for this variant in affected families.
PP3 SpliceAI predicts no significant splice impact (max delta score = 0.02).
PP4 No detailed patient phenotype or family history data are available to assess specificity for EZH2-related Weaver syndrome.
PP5 ClinVar classification for this variant is Likely benign (single submitter, Labcorp Genetics).
Benign
BA1 gnomAD allele frequency (0.0045%) is well below the 1% BA1 threshold.
BS1 gnomAD allele frequency (0.0045%) is well below the 0.3% BS1 threshold.
BS2 No documented observation of this variant in a healthy adult individual with full penetrance expected at an early age is available beyond population database frequencies.
BS3 No well-established functional studies demonstrate no damaging effect of this variant on splicing or protein function.
BS4 No segregation data available to assess lack of segregation with disease in affected families.
BP2 No observation of this variant in trans with a known pathogenic dominant EZH2 variant is available.
BP5 No observation of this variant in an individual with an alternate molecular basis for Weaver syndrome or EZH2-related overgrowth is available.
N/A · 7 PVS1 · PS1 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency · supports benign
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 4.53907e-05; MAF= 0.00454%, 73/1608258 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.94113e-05; MAF= 0.00594%, 70/1178228 alleles, homozygotes = 0); grpmax FAF= 4.788e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 4.46124e-05; MAF= 0.00446%, 11/246568 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.74003e-05; MAF= 0.00974%, 11/112936 alleles, homozygotes = 0); grpmax FAF= 5.414e-05.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0045% · 73 / 1,608,258
0 hom · FAF 0.0048%
European (non-Finnish)
70 / 1,178,228
0.0059%
Remaining individuals
2 / 62,414
0.0032%
South Asian
1 / 91,016
0.0011%
+ 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0045% · 11 / 246,568
0 hom · FAF 0.0054%
European (non-Finnish)
11 / 112,936
0.0097%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Likely benign (1 clinical laboratory). (ClinVarID = 416828)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
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
Triaged references · 2 PMIDs not cited in assessment
23865096 ↗ EZH2-Related Overgrowth. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR