HRAS c.7G>A, p.(Glu3Lys)

Reasoning

PM2 is met at supporting strength because NM_005343.4:c.7G>A is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. This satisfies the HRAS VCEP requirement that the variant be absent from controls in gnomAD.

Rule

The variant must be absent from controls (gnomAD).

Evidence considered

• The HRAS ClinGen RASopathy VCEP framework specifies PM2 at supporting strength when the variant is absent from controls in gnomAD.
• The variant is reported as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.

Sources

Reasoning

The HRAS VCEP restricts PM1 to variants within four critical, well-established functional domains: P-loop (AA 10-17), Switch I (AA 25-40), Switch II (AA 57-64), and SAK (AA 145-156). Glu3 (codon 3) falls outside all four of these domain boundaries, so PM1 is not met under the gene-specific specification.

Rule

HRAS VCEP cspec v2.3 PM1: variant located in P-loop, SW1, SW2, or SAK domain — Strength: Moderate.

Evidence considered

• cspec (HRAS VCEP v2.3) PM1 rule: 'Applicable only to critical and well-established functional domains available in the supplementary table (P-loop [AA 10-17], SW1 [AA 25-40], SW2 [AA 57-64], SAK [AA 145-156]). Not applicable to specific amino acid residues (see PM5).'
• Variant residue is Glu3 (codon 3), which lies outside the P-loop (10-17), Switch I (25-40), Switch II (57-64), and SAK (145-156) domain ranges defined by the VCEP supplementary alignment table (vcep_alignment_with_pm1_domains_pptx).

Sources

Reasoning

PM5 requires one or more different established [likely] pathogenic amino acid changes at the same codon (codon 3) as the variant under review. The codon-3 comparator search (pm5_candidates.json) using ClinVar queries for E3/Glu3 at codon 3 returned zero candidates, indicating no established pathogenic or likely pathogenic residue change has been reported at this codon.

Rule

HRAS VCEP cspec v2.3 PM5: 1 established [likely] pathogenic residue change at same codon = Moderate; ≥2 different changes in ≥5 probands = Strong.

Evidence considered

• pm5_candidates.json: 'candidate_summary.same_residue_candidates': 0; 'recommendation.summary': 'No clearly useful same-residue comparator variants were identified.'
• cspec (HRAS VCEP v2.3) PM5 rule: Strong for ≥2 different [likely] pathogenic residue changes at the same codon in ≥5 probands; Moderate for 1 such change.

Still missing

• Search was limited to ClinVar; no independent search of literature or other pathogenicity databases for alternate codon-3 substitutions was performed in this case.

Sources

Reasoning

Variant NM_005343.4:c.7G>A (p.(Glu3Lys)) is missense. Per HRAS VCEP (ClinGen RASopathy Expert Panel v2.3) PP3 rule, REVEL >= 0.7 is required for missense variants; REVEL score is 0.412, below threshold, so PP3 is not met via the missense path. For the splicing path, VCEP requires predicted splicing outcome to match disease mechanism; SpliceAI/Pangolin predicts no significant splice impact (max delta score = 0.00), so PP3 is not met via the splicing path either. BayesDel score is present in prefetch data but has no verified published calibration threshold available to this pipeline and is therefore treated as not_available/insufficiently calibrated for PP3, consistent with pipeline policy on unverified predictors.

Rule

HRAS VCEP (ClinGen RASopathy EP v2.3) PP3: missense REVEL >= 0.7 (Supporting); splicing outcome must match disease mechanism (Supporting)

Evidence considered

• HRAS VCEP (ClinGen RASopathy EP v2.3) PP3 rule: for missense variants, REVEL >= 0.7 required; REVEL score for this variant is 0.412 (below threshold).
• HRAS VCEP PP3 splicing-path rule requires predicted splicing outcome to match disease mechanism; SpliceAI/Pangolin lookup shows max delta score = 0.00 (no significant splice impact predicted).
• BayesDel score (-0.0436825) is available from local BayesDel_170824_noAF lookup but excluded from PP3 assessment because no verified published calibration threshold/publication is available to this pipeline for this predictor.

Sources

Reasoning

BA1 is not met because NM_005343.4:c.7G>A is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore its filtering allele frequency is not at or above the HRAS VCEP threshold of 0.05%.

Rule

GnomAD filtering allele frequency >=0.05%.

Evidence considered

• The HRAS ClinGen RASopathy VCEP framework specifies BA1 at stand-alone strength when the gnomAD filtering allele frequency is >=0.05%.
• The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no population allele frequency meets the BA1 threshold.

Sources

Reasoning

BS1 is not met because NM_005343.4:c.7G>A is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore its filtering allele frequency is not at or above the HRAS VCEP threshold of 0.025%.

Rule

GnomAD filtering allele frequency >=0.025%.

Evidence considered

• The HRAS ClinGen RASopathy VCEP framework specifies BS1 at strong strength when the gnomAD filtering allele frequency is >=0.025%.
• The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no population allele frequency meets the BS1 threshold.

Sources

Reasoning

Per HRAS VCEP BP4 rule, missense variants require REVEL <= 0.3 for BP4 to apply. REVEL score is 0.412, which is above the BP4 threshold and also below the PP3 threshold (0.7), placing it in the indeterminate zone where neither PP3 nor BP4 applies via the missense in-silico path. SpliceAI max delta score = 0.00 indicates no splice impact prediction, which alone does not satisfy the VCEP's BP4 criterion (the VCEP does not define a distinct BP4 splicing sub-rule; BP4 here is scoped to the missense REVEL threshold). BayesDel is not used (no verified published threshold available to this pipeline).

Rule

HRAS VCEP (ClinGen RASopathy EP v2.3) BP4: missense REVEL <= 0.3 (Supporting)

Evidence considered

• HRAS VCEP BP4 rule: for missense variants, REVEL <= 0.3 required; REVEL score for this variant is 0.412, which exceeds the BP4 threshold.
• REVEL score 0.412 falls between the BP4 (<=0.3) and PP3 (>=0.7) thresholds, so neither criterion is met under the VCEP-specified REVEL cutoffs.
• SpliceAI/Pangolin lookup shows max delta score = 0.00, consistent with no predicted splice disruption, but the VCEP framework does not define a separate BP4 splicing sub-threshold distinct from PP3's splicing-mechanism-match rule.

Sources

Reasoning

The HRAS VCEP (cspec v2.3) PS1 rule requires the same amino acid change as a previously established pathogenic variant, or an observed analogous residue change in HRAS, KRAS, MRAS, NRAS, RIT1, or RRAS2. p.(Glu3Lys) is absent from ClinVar and the codon-3 comparator search (pm5_candidates.json, ClinVar queries for E3/Glu3 at any amino acid substitution) returned zero candidates, so no established pathogenic same-AA-change comparator in HRAS itself was found. However, no paralog-gene (KRAS/NRAS/MRAS/RIT1/RRAS2) analogous-residue search was performed in this case bundle, which the VCEP rule explicitly allows as an alternative basis for PS1.

Rule

HRAS VCEP cspec v2.3 PS1: same amino acid change as an established pathogenic variant (any nucleotide change), or an analogous residue change observed in HRAS/KRAS/MRAS/NRAS/RIT1/RRAS2 — Strength: Strong.

Evidence considered

• cspec (HRAS VCEP v2.3) PS1 rule: 'Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Applicable for observed analogous residue positions in HRAS, KRAS, MRAS, NRAS, RIT1, and RRAS2.'
• pm5_candidates.json comparator search (ClinVar queries 'HRAS[GENE] AND E3[VARNAME]', 'HRAS[GENE] AND Glu3[VARNAME]', 'HRAS[GENE] AND p.Glu3[All Fields]') returned zero candidates at codon 3 in HRAS.
• clinvar source shows this variant (c.7G>A / p.Glu3Lys) itself is absent from ClinVar (evidence_sentence: 'This variant is absent from ClinVar.').

Still missing

• No search of KRAS/NRAS/MRAS/RIT1/RRAS2 for an established pathogenic variant at the analogous residue to HRAS Glu3 was performed or captured in the evidence bundle.
• No literature (PMID) evidence available in this case to confirm or refute a prior established pathogenic classification for p.(Glu3Lys) or an analogous paralog substitution.

Sources

Reasoning

The governing HRAS ClinGen RASopathy VCEP framework applies PS2 using SVI point-based scoring, with 4 points for Very Strong, 2 points for Strong, and 1 point for Moderate evidence. The case-evidence bundle contains no proband-level de novo observation, parental maternity and paternity testing, family history, or phenotype-specific information sufficient to establish and score PS2.

Rule

HRAS VCEP PS2: 4 points = Very Strong; 2 points = Strong; 1 point = Moderate; apply SVI recommendations with phenotype-based point adjustment.

Evidence considered

• The HRAS VCEP framework states that PS2 requires de novo evidence with maternity and paternity confirmation and specifies point-based strengths of 4, 2, or 1 points.
• The consolidated case-evidence bundle provides no case-specific proband, parental-testing, phenotype, or family-history evidence for this variant.

Still missing

• Proband-level report confirming the variant
• Documented maternity and paternity confirmation or informative parental testing
• Relevant RASopathy phenotype and clinical assessment
• Family history demonstrating absence of an inherited disease pattern

Sources

Reasoning

No functional assay data for NM_005343.4:c.7G>A (p.Glu3Lys) was identified in any case source. The literature pass returned zero PMIDs and fulltext_map is empty, so no published functional study could be screened against the RASopathy VCEP's approved assay list (SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx: RAS activation, MEK activation, ERK activation, and cell survival assays). OncoKB was queried variant-specifically (HRAS/E3K) but explicitly returned no variant-specific reviewed functional evidence, only gene-level cancer context. Per the HRAS VCEP framework, PS3 requires results from one or more of these approved assay types with defined validation controls; none are present for this variant.

Rule

HRAS VCEP v2.3 PS3: Supporting for one approved assay, Moderate for two or more different approved assays (RAS/MEK/ERK activation or cell survival assays per SVI-RASopathy-VCEP-V2-Approved-Functional-Studies.xlsx); no eligible assay data available for this variant.

Evidence considered

• OncoKB query for HRAS E3K returned 'Unknown Oncogenic Effect' with not_reviewed=true and is_variant_specific=false, i.e. no variant-specific functional assay evidence available.
• literature_pass.json reports total_pmids=0 and 'No PMIDs found across evidence sources', so no functional-study literature could be reviewed.
• fulltext_map.json is empty, confirming no full-text papers were retrieved for functional-assay screening.

Still missing

• No functional/biochemical assay publication identified for HRAS c.7G>A (p.Glu3Lys)
• OncoKB has no variant-specific functional classification for this variant
• No PMIDs surfaced by literature pass to screen for RAS activation, MEK/ERK phosphorylation, or cell survival assay data

Sources

Reasoning

No case-control enrichment dataset, affected-case count, or statistically interpretable comparison of affected individuals versus controls was provided for NM_005343.4:c.7G>A. The HRAS VCEP framework defines PS4 thresholds of at least 1 point for Supporting, at least 3 points for Moderate, and at least 5 points for Strong; no points can be assigned from the available evidence.

Rule

HRAS VCEP v2.3 PS4: Strong >=5 points; Moderate >=3 points; Supporting >=1 point.

Evidence considered

• The applicable HRAS VCEP Version 2.3 framework specifies PS4 as Supporting at >=1 point, Moderate at >=3 points, and Strong at >=5 points.
• The consolidated case-evidence bundle contains no case-control analysis, informative affected-proband count, or phenotype prevalence dataset for NM_005343.4:c.7G>A.

Still missing

• Case-control or validated case-enrichment data for the exact variant
• Count and phenotype-confirmation details for informative affected probands

Sources

Reasoning

The governing HRAS ClinGen RASopathy VCEP framework applies PM6 using SVI point-based scoring for an assumed de novo variant without confirmation of maternity and paternity: 2 points for Strong, 1 point for Moderate, and 0.5 points for Supporting evidence. The bundle contains no proband-level observation, parental genotypes, or phenotype information establishing an assumed de novo event.

Rule

HRAS VCEP PM6: 2 points = Strong; 1 point = Moderate; 0.5 points = Supporting; apply SVI recommendations with phenotype-based point adjustment.

Evidence considered

• The HRAS VCEP framework defines PM6 as assumed de novo evidence without confirmation of maternity and paternity and specifies 2, 1, and 0.5 point strengths.
• The consolidated case-evidence bundle provides no case-specific proband, parental-testing, or phenotype evidence from which PM6 points can be assigned.

Still missing

• Proband-level report confirming the variant
• Parental genotype results or documentation that maternity and paternity were not confirmed
• Relevant RASopathy phenotype and clinical assessment
• Assessment excluding an inherited familial variant

Sources

Reasoning

The governing HRAS ClinGen RASopathy VCEP framework applies PP1 for cosegregation and recommends segregation in more than one family. It assigns Supporting evidence at 3 or more informative meioses, Moderate at 5 or more, and Strong at 7 or more. No affected relatives, unaffected relatives, parental genotypes, informative meioses, or phenotype-segregation data are provided in the case-evidence bundle.

Rule

HRAS VCEP PP1: >=3 informative meioses = Supporting; >=5 = Moderate; >=7 = Strong; segregation in more than one family is recommended.

Evidence considered

• The HRAS VCEP framework recommends segregation in more than one family and defines PP1 thresholds of at least 3 informative meioses for Supporting, at least 5 for Moderate, and at least 7 for Strong.
• The consolidated case-evidence bundle contains no family segregation or informative-meiosis observations for this variant.

Still missing

• Affected relatives with confirmed diagnoses and variant testing
• Unaffected informative relatives with variant testing
• Count and phase of informative meioses
• Phenotype consistency for each tested relative
• Segregation data from more than one family if available

Sources

Reasoning

BS2 cannot be assessed from the case evidence bundle because no healthy adult homozygote or heterozygote observations, zygosity information, or phenotype/penetrance data are provided for this variant.

Rule

Strength adjustment using point-based scoring based on phenotypic specifications; healthy homozygote or heterozygote observations are required.

Evidence considered

• The HRAS ClinGen RASopathy VCEP framework permits BS2 using point-based scoring based on healthy homozygote or heterozygote individuals and reduced points for apparently unaffected heterozygotes, but the case bundle contains no such observations for this variant.

Still missing

• No documented healthy adult carrier or homozygote observations with zygosity and phenotype information were identified.
• No penetrance or age-of-onset information is available to determine whether an apparently unaffected individual is informative for the autosomal-dominant HRAS RASopathy context.

Sources

Reasoning

The governing HRAS ClinGen RASopathy VCEP framework defines BS4 as lack of segregation in affected family members and allows Strong evidence with one informative meiosis. The bundle contains no affected relatives, family genotypes, informative meioses, phenotype assessments, or evidence of non-segregation. Therefore BS4 cannot be applied or excluded from the available data.

Rule

HRAS VCEP BS4: lack of segregation in affected family members; Strong requires only one informative meiosis, with consideration of phenocopies and alternative pathogenic causes.

Evidence considered

• The HRAS VCEP framework defines BS4 as lack of segregation in affected family members and specifies Strong evidence with one informative meiosis.
• The consolidated case-evidence bundle contains no family testing or non-segregation evidence for this variant.

Still missing

• Affected family members tested for the variant
• Documented non-segregation in at least one informative meiosis
• Phenotype assessment and exclusion of phenocopies
• Assessment for an alternative pathogenic variant or other molecular cause

Sources

Reasoning

The HRAS Version 2.3 VCEP framework permits BP2 using its point-based thresholds (Supporting: ≥−1 point, Moderate: ≥−2 points, Strong: ≥−4 points), but the case bundle contains no affected-proband or family observations documenting the variant in trans with a pathogenic/likely pathogenic variant, no phase information, and no qualifying allelic observations. BP2 therefore cannot be assessed.

Rule

Supporting: ≥−1 point; Moderate: ≥−2 points; Strong: ≥−4 points.

Evidence considered

• The HRAS Version 2.3 VCEP rule for BP2 assigns Supporting, Moderate, and Strong levels at ≥−1, ≥−2, and ≥−4 points, respectively.
• The consolidated case-evidence bundle contains no PMIDs, no family or proband segregation records, and no phase, cis/trans, or second-variant observations relevant to BP2.

Still missing

• Documented affected-proband or family data showing the variant in trans with a pathogenic or likely pathogenic variant, with phase established, are absent.

Sources

Reasoning

The applicable HRAS VCEP Version 2.3 provides a point-based BP5 rule, but the supplied case-evidence bundle contains no documented alternate molecular diagnosis or other pathogenic variant in the same patient with a phenotype explaining the indication. BP5 therefore cannot be scored from the available evidence.

Rule

HRAS VCEP v2.3 BP5: Strong >=(-4) points; Moderate >=(-2) points; Supporting >=(-1) point.

Evidence considered

• The HRAS VCEP Version 2.3 specifies BP5 as Supporting at >=-1 point, Moderate at >=-2 points, and Strong at >=-4 points.
• No alternate pathogenic molecular diagnosis or patient-level phenotype-explanatory variant was documented in the consolidated case-evidence bundle.

Still missing

• Complete patient-level testing results for alternate molecular diagnoses
• Evidence that another pathogenic variant explains the patient's phenotype

Sources