Variant classification summary

NM_005228.4:c.2314_2319dup

EGFR · NP_005219.2:p.(Pro772_His773dup) · NM_005228.4

GRCh37: chr7:55249013 A>AACCCCC · GRCh38: chr7:55181320 A>AACCCCC

Gene: EGFR Transcript: NM_005228.4

Final call

VUS

PM1 moderate PM2 supporting PM4 moderate

Variant details

Gene

EGFR

Transcript

NM_005228.4

Protein

NP_005219.2:p.(Pro772_His773dup)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_005228.4:c.2314_2319dup (p.Pro772_His773dup) is an in-frame duplication in exon 20 of the EGFR tyrosine kinase domain, a critical functional domain where exon 20 insertions and duplications are established oncogenic gain-of-function mutations.

2

This variant is absent from gnomAD v2.1 and v4.1 population databases (0 alleles observed), consistent with a rare variant not present in the general population.

3

The variant has been reported 7 times in somatic cancers (COSMIC COSV51810066) and is classified as Likely Oncogenic with Likely Gain-of-function by OncoKB.

4

No variant-specific functional studies were identified in the literature. The sole functional paper reviewed (PMID:24353160) characterized six other EGFR exon 20 insertion variants but did not include p.Pro772_His773dup.

5

SpliceAI predicts no significant splicing impact for this variant (max delta score 0.03). REVEL and BayesDel scores are not available for this non-SNV variant.

6

The variant is absent from ClinVar with no pathogenic or benign classifications from any submitter.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	Not met	NM_005228.4:c.2314_2319dup is an in-frame duplication in exon 20 that does not fall into the ClinGen SVI PVS1 null-variant buckets (nonsense, frameshift, or canonical ±1,2 splice consensus variants). The generic PVS1 framework does not apply to this variant type.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	This variant is absent from ClinVar and no pathogenic variant with the identical amino acid change (p.Pro772_His773dup) has been reported. There is no same-amino-acid comparator to satisfy PS1.	clinvar
PS2	Not assessed	No de novo data available for this variant. No parental testing or trio analysis reported in any reviewed source.
PS3	Not met	No variant-specific functional data are available for NM_005228.4:c.2314_2319dup (p.Pro772_His773dup). The sole functional paper reviewed (PMID:24353160) characterized other exon 20 insertion variants (Y764_V765insHH, M766_A767insAI, A767_V769dupASV, D770_N771insNPG, D770_N771insSVD, H773_V774insH) but did not test or report this exact variant. OncoKB annotates this variant as Likely Oncogenic with Likely Gain-of-function, but curated database annotation alone does not constitute primary functional evidence for PS3 without variant-specific experimental data in the case folder.	PMID:24353160 oncokb
PS4	Not assessed	No case-control or prevalence data available for this variant in the germline setting.
PS5	N/A	PS5 requires a known pathogenic variant at the same amino acid residue. This is an in-frame duplication (not a missense change), and no comparator pathogenic variants were identified at residues 772-773.
PM1	Met	The variant p.Pro772_His773dup is located in exon 20 of EGFR, within the N-lobe of the tyrosine kinase domain (C-helix region, residues 762–774). Exon 20 of EGFR is a well-established mutational hotspot and critical functional domain where in-frame insertions and duplications are known to be oncogenic (Yasuda et al. 2013, PMID:24353160). The variant is absent from population databases, consistent with the 'without benign variation' requirement.	PMID:24353160 oncokb gnomad_v2 gnomad_v4
PM2	Met	This variant is absent from gnomAD v2.1 (exomes) and gnomAD v4.1 (exomes), consistent with a rare variant not observed in population databases. Under generic ACMG/AMP 2015 rules, allele frequency below 0.1% supports PM2.	gnomad_v2 gnomad_v4
PM3	N/A	Skipped per case instructions.
PM4	Met	NM_005228.4:c.2314_2319dup is a 6-nucleotide in-frame duplication resulting in the insertion of two amino acids (Pro772_His773dup) within exon 20 of the EGFR kinase domain, which is not a repetitive region. This protein length alteration due to in-frame duplication in a non-repeat region satisfies PM4 under generic ACMG/AMP 2015.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a novel missense change at an amino acid residue where a different missense change has been established as pathogenic. This variant is an in-frame duplication, not a missense substitution. No same-residue comparator variants were identified in the PM5 candidate search. PM5 semantics cannot be applied to this variant class.	pm5_candidates
PM6	Not assessed	No de novo data available for this variant. No confirmed de novo occurrence reported in any reviewed source.
PP1	Not assessed	No segregation data available for this variant. No family studies or cosegregation analyses were identified.
PP2	N/A	PP2 specifically applies to missense variants in genes with a low rate of benign missense variation where missense variants are a common disease mechanism. NM_005228.4:c.2314_2319dup is an in-frame duplication, not a missense variant.
PP3	Not met	Computational evidence does not support a deleterious effect. SpliceAI predicts no significant splice impact (max delta score 0.03). REVEL and BayesDel scores are unavailable for this non-SNV variant. No in silico tools predict a damaging effect on the gene product.	spliceai
PP4	Not assessed	No patient phenotype or clinical data were provided for this case. PP4 requires that the patient's phenotype or family history is highly specific for the disease associated with the gene.
PP5	Not met	This variant is absent from ClinVar. No reputable source has reported this variant as pathogenic. PP5 requires a reputable source (e.g., clinical diagnostic laboratory with appropriate quality control metrics) to have recently reported the variant as pathogenic.	clinvar
BA1	Not met	This variant is absent from gnomAD v2.1 and v4.1, with an allele frequency of 0%, far below the BA1 threshold of >1% in population databases.	gnomad_v2 gnomad_v4
BS1	Not met	This variant is absent from gnomAD v2.1 and v4.1, with an allele frequency of 0%, far below the BS1 threshold of >0.3% in population databases.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data available on observation of this variant in healthy adults. BS2 requires observation of the variant in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in an autosomal recessive disorder, or in homozygous state for a dominant disorder in unaffected individuals.
BS3	Not met	No well-established functional studies show a neutral or benign effect for this variant. The only functional evidence reviewed (PMID:24353160) characterized exon 20 insertions as gain-of-function/activating, which is the opposite of a benign functional effect. OncoKB annotates this variant as Likely Oncogenic with Likely Gain-of-function.	PMID:24353160 oncokb
BS4	Not assessed	No segregation data available for this variant. BS4 requires lack of segregation with disease in affected family members.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. NM_005228.4:c.2314_2319dup is an in-frame duplication, not a missense variant. Additionally, EGFR disease mechanisms include both gain-of-function (oncogenic) and loss-of-function contexts.
BP2	N/A	BP2 requires observation of the variant in trans with a known pathogenic dominant variant, or in cis with a pathogenic recessive variant. No such data are available or relevant to this case. The variant is absent from population databases making this criterion inapplicable.
BP3	N/A	BP3 applies to in-frame deletions or insertions in repetitive regions without known function. The p.Pro772_His773dup variant is located in exon 20 of the EGFR tyrosine kinase domain, which is neither a repetitive region nor without known function. The EGFR kinase domain is one of the most well-characterized functional domains in oncology.
BP4	Not met	Multiple lines of computational evidence are required to suggest no impact on the gene product. The only available computational data is SpliceAI (max delta 0.03, no predicted splicing impact). REVEL and BayesDel are unavailable for this non-SNV variant. A single computational tool is insufficient to satisfy the 'multiple lines of evidence' requirement for BP4.	spliceai
BP5	N/A	BP5 requires an alternate molecular basis for disease to have been identified in the case. No case-level data (phenotype, alternate genetic findings) were provided.
BP6	N/A	BP6 requires a reputable source to have recently reported the variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation. This variant is absent from ClinVar; no benign classification exists from any source.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact on the splice consensus sequence or a new splice site, and the nucleotide is not highly conserved. NM_005228.4:c.2314_2319dup is an in-frame duplication, not a synonymous variant.

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