EGFR c.2155G>A, p.(Gly719Ser)

Reasoning

No EGFR-specific VCEP/CSPEC was available, so generic ACMG/AMP functional-evidence guidance was applied. The exact variant EGFR p.G719S was tested in multiple biologically relevant, disease-mechanism-consistent systems with appropriate comparator contexts. In NIH-3T3 and hTBE cells, p.G719S caused ligand-independent oncogenic transformation, anchorage-independent growth, constitutive EGFR/downstream signaling, and tumor formation in immunocompromised mice; transformation was inhibited by erlotinib (PMID:16187797). Independently, in Ba/F3 cells, p.G719S caused IL-3-independent proliferation, constitutive receptor and downstream phosphorylation, and gefitinib-sensitive growth inhibition, with a reported gefitinib IC50 of approximately 140 nmol/L (PMID:16204070). A separate MANO Ba/F3 functional screen also classified G719S among TKI-sensitive EGFR mutants with dose-dependent death after EGFR-TKI exposure, with supporting xenograft depletion after erlotinib (PMID:29141884). These concordant results directly demonstrate abnormal activating function for the tested variant; the assay systems, pathway readouts, pharmacologic controls/comparators, and in vivo corroboration support strong rather than moderate PS3.

Rule

Generic ACMG/AMP PS3: well-established functional studies supportive of a damaging effect; strength calibrated as strong when multiple concordant, biologically relevant, well-controlled assays directly test the exact variant.

Evidence considered

• PMID:16187797 directly tested EGFR G719S in NIH-3T3 and hTBE cells: the mutant caused ligand-independent transformation, anchorage-independent growth, constitutive EGFR/STAT3/Akt signaling, and tumors in immunocompromised mice; erlotinib inhibited the phenotype.
• PMID:16204070 directly tested EGFR-G719S in Ba/F3 cells: the mutant conferred IL-3-independent growth and constitutive EGFR, STAT5, ERK1/2, ERK5, and AKT phosphorylation; gefitinib inhibited growth with an approximately 140 nmol/L IC50.
• PMID:29141884 independently evaluated EGFR G719S in a MANO Ba/F3 assay and reported dose-dependent death with multiple EGFR TKIs, with additional xenograft depletion after erlotinib.
• The concordant gain-of-function results across independent cellular systems, orthogonal signaling/proliferation/transformation readouts, pharmacologic comparator conditions, and an in vivo xenograft experiment meet generic ACMG/AMP PS3 strong-level functional evidence expectations.

Sources

Reasoning

No applicable EGFR VCEP specification or authoritative domain table was retrieved, so the generic ACMG/AMP PM1 rule applies. EGFR p.Gly719Ser lies in the tyrosine-kinase ATP-binding loop (p-loop), a critical functional region; the reviewed functional study explicitly places G719S in that loop and demonstrates constitutive receptor signaling and transforming activity. The case evidence also identifies residue G719 as a statistically significant cancer hotspot. Together these support PM1 at the generic moderate level, while no VCEP-specific strength adjustment is available.

Rule

generic_acmg_2015: PM1_moderate_for_critical_functional_domain_or_hotspot_without_benign_variation

Evidence considered

• PMID:16204070 describes EGFR-G719S as located in the ATP-binding loop (p-loop) and reports constitutive receptor autophosphorylation, downstream signaling, and ligand-independent transformation.
• The Cancer Hotspots result identifies EGFR G719 as a statistically significant hotspot; the structured extraction is partially parsed but the corresponding screenshot is available for audit.
• No EGFR-specific VCEP domain table was available; therefore no authoritative domain-table exclusion or alternative strength rule could be applied.

Sources

Reasoning

PM2 is met at supporting strength. NM_005228.4:c.2155G>A (EGFR p.Gly719Ser) is absent from gnomAD v2.1 and gnomAD v4.1, and the available non-cancer subset checks also report absence; this is consistent with an observed allele frequency <=0.0001. No applicable EGFR-specific VCEP specification was available, so the generic ClinGen SVI recommendation to apply PM2 only at supporting strength was used.

Rule

Generic PM2: absent or rare in population databases at observed allele frequency <=0.0001; apply at supporting strength under the ClinGen SVI recommendation when no VCEP rule governs.

Evidence considered

• The variant is reported absent from gnomAD v2.1 (GRCh37) and gnomAD v4.1 (GRCh38).
• The available gnomAD evidence also reports absence from the gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets.
• The generic PM2 threshold of <=0.0001 and supporting-only strength were used under the ClinGen SVI recommendation described in the supplied calibration block, based on Richards et al. 2015 (PMID:25741868), because no EGFR-specific VCEP rule was available.

Sources

Reasoning

The variant is an exonic missense substitution, NM_005228.4:c.2155G>A (p.Gly719Ser), so the missense computational path is applicable. REVEL is 0.853, which meets the generic ClinGen SVI moderate PP3 threshold of >=0.773 from the supplied Pejaver et al. 2022 calibration (PMID:36413997). BayesDel is not used because no generic ACMG strength calibration is established for that score. SpliceAI is not evaluated for this exonic missense adjudication because the splice-impact path is scoped to splice-region or intronic variants.

Rule

Generic ClinGen SVI REVEL calibration: PP3 moderate at REVEL >=0.773; governing EGFR-specific specification not available.

Evidence considered

• The case evidence reports REVEL 0.853 for NM_005228.4:c.2155G>A (p.Gly719Ser).
• The supplied ClinGen SVI REVEL calibration assigns PP3 moderate at REVEL >=0.773 (Pejaver et al. 2022, PMID:36413997).
• The variant is classified as missense, making the missense computational path applicable; BayesDel has no generic ACMG strength calibration and SpliceAI is reserved here for splice-region or intronic variants.

Sources

Reasoning

The exact-variant ClinVar record is NM_005228.5(EGFR):c.2155G>A (p.Gly719Ser), but the submission audit reports zero expert-panel submissions. The available Likely pathogenic assertion is from a non-expert clinical laboratory submission without assertion criteria, while other submissions are single-submitter laboratory or drug-response records. Under the specified rule, non-expert and aggregate ClinVar classifications cannot trigger PP5.

Evidence considered

• The exact ClinVar record contains one non-expert Likely pathogenic submission with no assertion criteria and no expert-panel classification.
• ClinVar submission audit counts expert_panel_submissions as 0; ordinary laboratory submissions and drug-response labels are excluded from PP5 by rule.

Sources

Reasoning

BA1 is not met. NM_005228.4:c.2155G>A (EGFR p.Gly719Ser) is absent from gnomAD v2.1 and gnomAD v4.1, including the reported non-cancer subsets, so its observed population frequency does not reach the generic stand-alone BA1 threshold of >=0.05. No EGFR-specific VCEP framework was available; the generic ACMG/AMP threshold is therefore applicable.

Rule

Generic ACMG/AMP BA1: stand-alone benign when allele frequency is >=0.05; no EGFR-specific VCEP rule was available.

Evidence considered

• The variant is reported absent from gnomAD v2.1 (GRCh37) and gnomAD v4.1 (GRCh38).
• The available gnomAD evidence also reports absence from the gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets.
• With no applicable EGFR-specific VCEP specification, the published generic ACMG/AMP BA1 threshold of >=0.05 from Richards et al. 2015 (PMID:25741868) was used.

Sources

Reasoning

BS1 is not met. NM_005228.4:c.2155G>A (EGFR p.Gly719Ser) is absent from gnomAD v2.1 and gnomAD v4.1, including the reported non-cancer subsets, and therefore has no observed allele frequency reaching the generic BS1 threshold of >=0.01. No EGFR-specific VCEP framework was available; the generic threshold was used.

Rule

Generic BS1: strong benign when allele frequency is >=0.01; no EGFR-specific VCEP rule was available.

Evidence considered

• The variant is reported absent from gnomAD v2.1 (GRCh37) and gnomAD v4.1 (GRCh38).
• The available gnomAD evidence also reports absence from the gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets.
• The generic BS1 threshold of >=0.01 was used because no applicable EGFR-specific VCEP threshold was available; this is the generic SVI default described by Whiffin et al. 2017 (PMID:28518168).

Sources

Reasoning

BS2 is not met. The available population data report no observations of NM_005228.4:c.2155G>A in gnomAD v2.1 or v4.1, including the reported non-cancer subsets; consequently, there is no evidence here that the variant occurs in healthy individuals or in healthy homozygotes. The somatic cancer reports are not BS2 evidence.

Rule

BS2 requires observation in healthy individuals, commonly including healthy homozygotes where relevant; no such observation is present.

Evidence considered

• The variant is reported absent from gnomAD v2.1 and gnomAD v4.1, with absence also reported for the available non-cancer subsets.
• No healthy individual or healthy homozygote carrying this variant is documented in the supplied population evidence.
• Cancer-database and tumor-study observations were not used for BS2 because they do not establish occurrence in healthy individuals.

Sources

Reasoning

No EGFR-specific VCEP/CSPEC was available, so generic ACMG/AMP guidance was applied. The available exact-variant functional studies do not demonstrate normal or benign function. Instead, EGFR p.G719S consistently shows activating, disease-relevant phenotypes: ligand-independent transformation and tumor formation in NIH-3T3/hTBE cells (PMID:16187797), IL-3-independent Ba/F3 growth with constitutive signaling (PMID:16204070), and TKI-sensitive abnormal growth in the MANO assay (PMID:29141884). Therefore, BS3 is not met; the evidence is directionally incompatible with a benign functional interpretation, although BS3 is not assigned a negative strength.

Rule

Generic ACMG/AMP BS3: well-established functional studies showing no damaging effect; not met when exact-variant assays instead demonstrate a disease-relevant abnormal effect.

Evidence considered

• PMID:16187797 reported ligand-independent transformation, constitutive signaling, and tumor formation for EGFR G719S, providing no benign-function result.
• PMID:16204070 reported IL-3-independent Ba/F3 proliferation and constitutive downstream signaling for EGFR-G719S, providing no normal-function result.
• PMID:29141884 classified EGFR G719S as TKI-sensitive based on abnormal mutant-cell viability responses, not as functionally equivalent to wild type.
• Because the available exact-variant assays show activating abnormal function rather than normal function, BS3 cannot be applied.

Still missing

• No exact-variant assay was identified that demonstrated normal function relative to an appropriate wild-type control for purposes of BS3.

Sources

Reasoning

BP1 is intended for genes in which truncating variants are the established disease mechanism and missense variants are not a common disease mechanism. The reviewed EGFR evidence instead documents recurrent activating missense variants in the kinase domain, including G719S, with ligand-independent signaling and transforming activity; therefore the prerequisite pattern for BP1 is not supported.

Rule

generic_acmg_2015: BP1_requires_truncation_dominant_gene_mechanism_with_missense_not_common

Evidence considered

• PMID:16187797 reports that EGFR G719S transforms NIH-3T3 cells and activates downstream signaling, directly supporting a disease-relevant activating missense mechanism.
• PMID:16204070 reports ligand-independent proliferation and constitutive EGFR signaling for G719S and places it in the ATP-binding loop.
• No reviewed evidence establishes truncating variants as the dominant relevant EGFR disease mechanism required by BP1.

Sources

Reasoning

The variant is an exonic missense substitution, NM_005228.4:c.2155G>A (p.Gly719Ser), so BP4 is assessed through the missense computational path. REVEL is 0.853, above all supplied generic benign BP4 thresholds (<=0.29 supporting, <=0.183 moderate, and <=0.016 strong), and therefore does not support BP4. BayesDel is not informative for BP4 because no generic ACMG strength calibration is established for that score. SpliceAI is not evaluated for this exonic missense adjudication because the splice-impact path is scoped to splice-region or intronic variants.

Rule

Generic ClinGen SVI REVEL calibration: BP4 supporting at REVEL <=0.29, moderate at <=0.183, or strong at <=0.016; governing EGFR-specific specification not available.

Evidence considered

• The case evidence reports REVEL 0.853 for NM_005228.4:c.2155G>A (p.Gly719Ser).
• The supplied ClinGen SVI REVEL calibration defines BP4 supporting at REVEL <=0.29, moderate at <=0.183, and strong at <=0.016 (Pejaver et al. 2022, PMID:36413997).
• The variant is classified as missense, making the missense computational path applicable; BayesDel has no generic ACMG strength calibration and SpliceAI is reserved here for splice-region or intronic variants.

Sources

Reasoning

The exact-variant ClinVar record is NM_005228.5(EGFR):c.2155G>A (p.Gly719Ser), and the submission audit reports zero expert-panel submissions. No exact-variant expert-panel classification of Benign or Likely benign is present; the available submissions are Uncertain significance, drug response, or non-expert Likely pathogenic. Therefore BP6 is not met under the specified expert-panel-only rule.

Evidence considered

• The exact ClinVar submission audit reports zero expert-panel submissions and no Benign or Likely benign expert-panel classification.
• Ordinary laboratory submissions, aggregate labels, and non-expert assertions are excluded from BP6 by rule.

Sources

Reasoning

No applicable EGFR VCEP specification was retrieved. The exact EGFR p.Gly719Ser change is reported in several publications, but the reviewed evidence does not establish that an independently observed same-amino-acid change is a known pathogenic variant; variant-specific oncogenic or drug-response labels cannot substitute for the PS1 requirement.

Rule

generic_acmg_2015: requires_same_amino_acid_change_previously_established_pathogenic

Evidence considered

• The reviewed papers explicitly report EGFR G719S, including functional transformation and clinical drug-response observations, but they do not provide an independent established pathogenic classification suitable for PS1.
• The exact variant is present in ClinVar with mixed or non-expert submission classifications rather than an expert-panel pathogenic assertion.

Still missing

• A validated pathogenic same-amino-acid comparator or applicable expert-panel classification is needed.

Sources

Reasoning

No proband-level de novo observation is documented. The available evidence describes somatic EGFR G719S findings in cancer specimens and functional studies, without parental testing, confirmed maternity and paternity, or phenotype-consistent clinical de novo evidence. Therefore PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no family history, with confirmed maternity and paternity for the strongest application.

Evidence considered

• The available case evidence contains somatic cancer observations and functional studies for EGFR p.Gly719Ser, but no proband pedigree, parental testing, or confirmed de novo event.
• Generic ACMG/AMP PS2 requires a confirmed de novo variant in a patient with an appropriate phenotype, with maternity and paternity established when applying the strongest evidence.

Still missing

• Proband phenotype and clinical diagnosis are not documented.
• Parental genotypes and confirmation of maternity and paternity are not documented.
• No validated de novo occurrence in the proband is documented.

Reasoning

No EGFR-specific VCEP framework was available, so generic ACMG/AMP PS4 was considered. The literature documents exact EGFR G719S observations in NSCLC, including two treated patients in a cohort of 1,261 NSCLC patients and one case in a sequencing series, but it does not provide a matched-control comparison, odds ratio, statistical significance, or a validated prevalence threshold for this exact variant. Aggregate G719X treatment outcomes are not exact-variant evidence and cannot establish PS4. The available evidence is therefore insufficient to assess case-control enrichment rather than evidence that enrichment is absent.

Evidence considered

• PMID:21531810 reports exact G719S in two patients with complex mutations and includes 15 patients with G719 mutations, with an aggregate response rate of 53.3% (8/15); this is not a case-control enrichment analysis.
• PMID:16199108 identifies exact G719S in one gefitinib-treated NSCLC sample, but provides no control prevalence or statistical enrichment analysis.
• PMID:23468066 identifies exact c.2155G>A/p.G719S in one NSCLC case with an observed allele frequency of 39.5%, without case-control enrichment statistics.

Still missing

• A case-control dataset specifically evaluating exact EGFR G719S is unavailable.
• No odds ratio, confidence interval, p-value, or governing threshold for PS4 is reported.

Sources

Reasoning

No applicable EGFR-specific VCEP specification was identified, so generic ACMG/AMP criteria were considered. PM3 requires the variant to be observed in trans with a pathogenic or likely pathogenic variant in an affected individual for a recessive disorder, with strength depending on the number and quality of such observations. The available evidence concerns somatic NSCLC tumors and functional or treatment-response studies; two reports mention EGFR G719S with additional EGFR variants, but neither establishes germline origin, affected-proband status, inheritance, or cis/trans phase. Therefore PM3 cannot be assessed from the available evidence.

Evidence considered

• PMID:21531810 reports EGFR G719S in two complex somatic NSCLC mutation profiles, including Q701L + I706T + G719S and G719S + L861Q, but does not establish germline origin, affected-proband status, or whether the variants are in trans.
• PMID:23468066 reports EGFR c.2155G>A/p.G719S together with c.2126A>C/p.E709A in a somatic NSCLC specimen, with an observed allele frequency of 39.5%, but provides no germline inheritance or cis/trans phasing.
• No EGFR-specific VCEP or CSPEC specification was available; generic ACMG/AMP PM3 logic therefore applies.

Still missing

• A confirmed germline affected individual with EGFR p.Gly719Ser is not documented.
• No pathogenic or likely pathogenic second EGFR allele is documented in trans.
• No parental testing, family segregation, or laboratory phasing establishes allele phase.

Sources

Reasoning

The reviewed evidence identifies alternate substitutions at residue 719 in the broader G719 group, including G719C and G719A, but does not establish either alternate as a known pathogenic germline variant under an applicable expert-panel or validated criterion-based classification. Functional or drug-sensitivity findings alone cannot satisfy the generic PM5 requirement.

Rule

generic_acmg_2015: requires_different_missense_change_at_same_residue_established_pathogenic

Evidence considered

• PMID:29141884 discusses G719C and G719A as alternate substitutions at residue 719 with differing tyrosine-kinase-inhibitor sensitivity, but it does not establish their ACMG pathogenic status.
• The PM5 candidate artifact contains no harvested same-residue candidates and explicitly warns that classic PM5 semantics could not be confirmed safely.

Still missing

• A same-residue alternate missense variant with a validated pathogenic classification is needed.

Sources

Reasoning

No proband-level de novo observation is documented without parental confirmation. The available literature concerns somatic EGFR G719S in tumors or experimental systems and does not provide an unconfirmed clinical de novo occurrence suitable for PM6. Therefore PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in a patient with the disease when parental testing is unavailable or incomplete, applied more cautiously than PS2.

Evidence considered

• The available case evidence reports EGFR p.Gly719Ser in somatic NSCLC samples and functional assays, not as an unconfirmed de novo germline observation in a clinically characterized proband.
• Generic ACMG/AMP PM6 is reserved for a presumed de novo occurrence when parental testing is unavailable or incomplete; no such clinical observation is documented here.

Still missing

• A clinical proband carrying the variant is not identified with a phenotype relevant to EGFR-associated disease.
• No parental testing or clinical statement of de novo status is documented.
• No clinical de novo observation lacking parental confirmation is available for PM6.

Reasoning

No affected relatives, informative meioses, or family segregation data are documented. The available evidence consists of tumor observations and functional studies rather than familial clinical observations. Consequently, cosegregation with disease cannot be evaluated and PP1 is not assessed.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members, with strength informed by the number and informativeness of meioses.

Evidence considered

• No family-level genotype–phenotype data, affected relatives, or informative meioses are present in the available evidence.
• Somatic tumor reports and in vitro or xenograft functional studies do not establish cosegregation with a familial clinical phenotype.

Still missing

• No family pedigree or affected relatives are documented.
• No familial genotypes or informative meioses are documented.
• No phenotype concordance across variant-positive relatives is documented.

Reasoning

PP2 requires gene-level evidence that missense variation is a common disease mechanism and benign missense variation is uncommon. The available material documents EGFR missense oncogenic activity and clinical cancer observations, but it does not provide a validated gene-level missense-versus-benign-variation analysis for the relevant disease context; a single variant's functional or oncogenic evidence cannot establish PP2.

Rule

generic_acmg_2015: requires_gene_level_common_pathogenic_missense_and_rare_benign_missense_pattern

Evidence considered

• The available publications concern individual EGFR missense variants, functional assays, or somatic treatment cohorts rather than a validated gene-level PP2 analysis.
• No applicable EGFR VCEP specification or gene-level missense constraint/resource was retrieved.

Still missing

• A disease-relevant gene-level analysis showing common pathogenic missense variation and rare benign missense variation is needed.

Sources

Reasoning

No EGFR-specific VCEP framework was available, so generic PP4 was considered. The available records describe EGFR G719S in somatic NSCLC cohorts and treatment-response studies, but they do not provide an individual patient's phenotype, a defined germline disease context, or a phenotype-specificity threshold demonstrating that the clinical presentation is highly specific for a disorder caused by this variant. Somatic cancer occurrence and aggregate G719X treatment response do not independently establish PP4.

Evidence considered

• The reviewed exact-variant papers concern somatic NSCLC detection or tyrosine-kinase-inhibitor response and do not establish a highly specific phenotype for a germline disorder.
• Aggregate G719X response data were not used as PP4 evidence because the papers do not specifically evaluate G719S phenotype specificity.

Still missing

• No individual clinical phenotype is supplied for this variant.
• No disease-specific phenotype specificity rule or threshold is available.

Sources

Reasoning

No clinically unaffected relatives have documented genotypes and phenotypes that could demonstrate non-segregation. The available evidence does not provide an informative family study or reliable unaffected-carrier observation, so BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation with disease in an informative family, such as absence of the variant in affected relatives, with phenotype and penetrance sufficiently established.

Evidence considered

• The available case evidence contains no informative unaffected relatives or family-level genotype–phenotype comparisons.
• Somatic cancer observations and functional assays cannot establish non-segregation of a germline variant with a familial disease phenotype.

Still missing

• No unaffected relatives with documented clinical phenotypes are identified.
• No genotypes for unaffected relatives are documented.
• No family structure or penetrance context is available to interpret non-segregation.

Reasoning

No applicable EGFR-specific VCEP specification was identified, so generic ACMG/AMP criteria were considered. BP2 requires observation of the variant in cis with a pathogenic or likely pathogenic variant, or in trans with a benign variant, with reliable phase and disease-context information. The available reports describe somatic NSCLC tumors containing EGFR G719S with additional EGFR variants, but they do not establish the clinical classification of the partner variants for BP2, germline origin, inheritance, or cis/trans phase. Therefore BP2 cannot be assessed from the available evidence.

Evidence considered

• PMID:21531810 reports G719S in complex somatic EGFR mutation profiles with Q701L + I706T or L861Q, but does not classify the partner variants as benign or pathogenic for BP2 and does not establish phase.
• PMID:23468066 reports G719S with EGFR p.E709A in a somatic NSCLC specimen, but does not establish whether the variants are in cis or trans or provide a benign classification for the partner allele.
• No EGFR-specific VCEP or CSPEC specification was available; generic ACMG/AMP BP2 logic therefore applies.

Still missing

• The clinical classification of any co-occurring allele is not established for BP2.
• No reliable cis or trans phasing is reported.
• The available co-occurrence observations are somatic tumor findings rather than documented germline inheritance data.

Sources

Reasoning

No EGFR-specific VCEP framework was available. The evidence reviewed for this group does not establish the BP5 situation of an affected individual having a clearly demonstrated alternative molecular basis for the relevant disease, and no patient-level alternate causal variant or validated exclusion framework is provided. The presence of EGFR G719S in somatic NSCLC or treatment-response cohorts cannot be treated as BP5 evidence.

Evidence considered

• The available exact-variant reports document EGFR G719S in somatic NSCLC samples or treatment cohorts, not an affected individual with a demonstrated alternative molecular basis for disease.

Still missing

• No patient-level phenotype and alternative molecular diagnosis are documented.
• No applicable EGFR-specific BP5 rule is available.