NM_004456.4:c.1852-9A>C

EZH2 · NP_004447.2:p.? · NM_004456.4

GRCh37: chr7:148508821 T>G · GRCh38: chr7:148811729 T>G

Gene: EZH2 Transcript: NM_004456.4

Final call

Likely Benign

PM2 supporting BP4 supporting benign BP6 supporting benign

Variant details

Gene

EZH2

Transcript

NM_004456.4

Protein

NP_004447.2:p.?

gnomAD AF

4.539072710970504e-05 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

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.

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).

SpliceAI predicts no significant splice impact (max delta score = 0.02), providing computational evidence that the variant does not disrupt normal splicing (BP4_supporting).

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).

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.

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.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Benign classification because either one strong benign criterion plus one supporting benign criterion, or at least two supporting benign criteria, are present.

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	Intronic variant (c.1852-9A>C) located outside canonical splice donor/acceptor ±1,2 consensus sites. Does not fall into PVS1 null-variant buckets (nonsense, frameshift, or canonical splice) per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_generic_framework
PS1	N/A	Intronic variant produces no amino acid change; cannot compare to a pathogenic missense change at the same residue.
PS2	Not assessed	No de novo observation for NM_004456.4:c.1852-9A>C was identified in the reviewed literature or ClinVar submissions.
PS3	Not assessed	No well-established functional studies evaluating the impact of this intronic variant on splicing or protein function were identified.
PS4	Not met	The variant has been observed in ClinVar as Likely benign (single submitter) and is present in gnomAD at low frequency (AF ~0.0045%). No case series or cohort study demonstrating enrichment in affected individuals was identified. Neither reviewed paper provides variant-specific case observations.	clinvar gnomad_v2 gnomad_v4
PS5	Not assessed	No reputable source has recently reported this variant as pathogenic with unavailable supporting evidence.
PM1	Not met	The variant is not located in a well-established mutational hotspot or critical functional domain. Hotspot assessment found no significant residue-level clustering and the exact variant is not listed in known hotspot catalogs.
PM2	Met	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 gnomad_v4
PM5	N/A	Intronic variant; no missense residue to compare. pm5_candidates.json confirms no classic same-residue PM5 semantics applicable.	pm5_candidates
PM6	Not assessed	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	Not assessed	No cosegregation data available for this variant in affected families.
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation. NM_004456.4:c.1852-9A>C is an intronic variant, not a missense change.
PP3	Not met	SpliceAI predicts no significant splice impact (max delta score = 0.02). No other computational evidence (REVEL, BayesDel unavailable for intronic variant) supports a deleterious effect. Multiple lines of computational evidence do not support pathogenicity.	spliceai
PP4	Not assessed	No detailed patient phenotype or family history data are available to assess specificity for EZH2-related Weaver syndrome.
PP5	Not met	ClinVar classification for this variant is Likely benign (single submitter, Labcorp Genetics). No reputable source reports this variant as pathogenic. The GeneReviews article on EZH2-Related Overgrowth (PMID:23865096) does not mention this specific variant in available sources.	clinvar
BA1	Not met	gnomAD allele frequency (0.0045%) is well below the 1% BA1 threshold.	gnomad_v2 gnomad_v4
BS1	Not met	gnomAD allele frequency (0.0045%) is well below the 0.3% BS1 threshold.	gnomad_v2 gnomad_v4
BS2	Not assessed	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	Not met	No well-established functional studies demonstrate no damaging effect of this variant on splicing or protein function. SpliceAI in silico prediction is addressed under BP4 and does not alone constitute BS3-level evidence.
BS4	Not assessed	No segregation data available to assess lack of segregation with disease in affected families.
BP1	N/A	BP1 applies to missense variants in genes where truncating variants are a known mechanism of disease. NM_004456.4:c.1852-9A>C is an intronic variant, not a missense change.
BP2	Not assessed	No observation of this variant in trans with a known pathogenic dominant EZH2 variant is available.
BP3	N/A	Skipped per instruction: trivially not_applicable. BP3 applies to in-frame deletions/insertions in repetitive regions; this is a single-nucleotide intronic substitution.
BP4	Met	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
BP5	Not assessed	No observation of this variant in an individual with an alternate molecular basis for Weaver syndrome or EZH2-related overgrowth is available.
BP6	Met	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
BP7	N/A	BP7 applies to synonymous (silent) coding variants with no predicted splice impact. NM_004456.4:c.1852-9A>C is an intronic variant, not a synonymous coding change.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.