The ARAF NM_001654.5:c.641C>G (NP_001645.1:p.(Ser214Cys)) missense variant has not previously been reported in somatic cancers (COSMIC), and lies in a statistically significant hotspot (cancerhotspots.org). Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.ARAF encodes a serine/threonine kinase in the RAF family that helps transmit RAS signals through the MAPK pathway, regulating cell growth, proliferation, and survival. It is associated with high-grade glioma and with certain cancers, including cholangiocarcinoma, lung, uterine, and histiocytic carcinomas. ARAF functions as an oncogene, and abnormal activation can promote cancer development and may create sensitivity to drugs targeting RAF or the MAPK pathway.
The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met at moderate strength: ARAF S214 is reported as a statistically significant hotspot, while the variant is absent from gnomAD v2.1 and v4.1.
Met at supporting strength: the variant is absent from gnomAD v2.1 and v4.1, below the <=0.0001 PM2 threshold.
No benign criterion marked as applied in the recorded assessment.
VUS: PM1 moderate plus PM2 supporting does not meet a generic ACMG/AMP pathogenic, likely pathogenic, benign, or likely benign combination.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
No SpliceAI or REVEL score is recorded in the fields used for this tile.
A ClinVar laboratory submission summary was not recorded.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant lies in a statistically significant hotspot.
ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.
28 criteria with recorded statuses: 2 met · 8 not met · 14 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Among the requested codon, residue, and domain criteria, only generic PM1 is supported by the reported ARAF S214 hotspot; PS1 and PM5 lack qualifying pathogenic comparators, while PP2 and BP1 lack required gene-level evidence.
No VCEP covers ARAF, so the generic ACMG/AMP rules supplied for this group govern.
The only variant-specific paper was checked for case-control evidence; it describes a functional somatic cancer study rather than an exact-variant affected-versus-control comparison.
PP5 and BP6 require exact-variant ClinVar expert-panel classifications, and the variant is absent from ClinVar.
No criteria match.
ARAF p.Ser214Cys lies at residue 214, and the Cancer Hotspots result identifies ARAF S214 as a statistically significant hotspot. Under the generic ACMG/AMP PM1 definition, a mutational hotspot is a qualifying route. The variant is absent from gnomAD v2.1 and gnomAD v4.1, providing no observed benign population variation for this exact variant. The hotspot extraction is marked as partially parsed and should be confirmed against the stored screenshot before final clinical sign-off.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
PM2 is met at supporting strength. NM_001654.5:c.641C>G (ARAF p.Ser214Cys) is absent from gnomAD v2.1 and gnomAD v4.1, and absence is also reported in the gnomAD v2.1 and v3.1 non-cancer subsets. This is below the generic PM2 supporting threshold of <=0.0001; no conflicting population observation is reported. The indel calling caveat does not apply because this variant is a single-nucleotide substitution.
PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868) ... Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
The variant is NP_001645.1:p.(Ser214Cys), but the available evidence identifies no previously established pathogenic variant producing the same amino-acid change through a different nucleotide change. ClinVar returned no exact record, and the only identified paper concerns this same somatic ARAF S214C variant rather than a prior established pathogenic comparator. Therefore PS1 is not met.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
The variant changes ARAF residue 214 from serine to cysteine. The available evidence does not establish a different missense change at residue 214 as pathogenic: the identified somatic report concerns the same S214C substitution, and no qualifying comparator was returned from the case's ClinVar or candidate evidence. The presence of a hotspot alone does not satisfy PM5, so PM5 is not met.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
Generic ACMG/AMP PP3 is applicable because NM_001654.5:c.641C>G is a missense variant, NP_001645.1:p.(Ser214Cys), and the governing generic path for a missense variant is REVEL only. REVEL is unavailable for this variant, so no calibrated PP3 threshold can be met. The recorded BayesDel score (0.125166) is not usable because no generic ACMG-strength calibration is established for BayesDel; the unavailable SpliceAI result is not an alternative path for a missense PP3 assessment. Therefore PP3 is not met.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent
The governing rule concerns a reputable recent report of the variant as pathogenic when the underlying evidence is unavailable for independent evaluation. The exact variant is absent from ClinVar, with no expert-panel Pathogenic or Likely pathogenic classification; the available OncoKB literature context is not an expert-panel ClinVar assertion and is somatic oncology evidence, so PP5 is not met.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BA1 is not met. NM_001654.5:c.641C>G (ARAF p.Ser214Cys) is absent from gnomAD v2.1 and gnomAD v4.1, so no allele frequency reaches the generic BA1 threshold of >=0.05. The available evidence also reports absence from the gnomAD v2.1 and v3.1 non-cancer subsets; no popmax point estimate or grpmax FAF is available, and therefore neither can support a BA1 call.
BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868) ... Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
BS1 is not met. The variant is absent from gnomAD v2.1 and v4.1, with absence also reported in the gnomAD v2.1 and v3.1 non-cancer subsets, so the available data provide no allele frequency greater than expected for the disorder and no frequency at or above the generic 0.01 default. Because no elevated frequency was observed, an ancestry-specific maximum-credible-frequency calculation is not triggered.
BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168) ... Allele frequency is greater than expected for the disorder.
Generic ACMG/AMP BP4 is applicable because NM_001654.5:c.641C>G is a missense variant, and the governing generic path for a missense variant is REVEL only. REVEL is unavailable, so no calibrated BP4 threshold can be met. The recorded BayesDel score (0.125166) is not usable because no generic ACMG-strength calibration is established for BayesDel; SpliceAI returned no score and is not the applicable path for a missense BP4 assessment. Therefore BP4 is not met.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion.
The governing rule concerns a reputable recent report of the variant as benign when the underlying evidence is unavailable for independent evaluation. The exact variant is absent from ClinVar, with no expert-panel Benign or Likely benign classification; ordinary literature or aggregate labels cannot trigger BP6, so BP6 is not met.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The available case materials do not provide a germline proband disease phenotype, family-history assessment, or testing results confirming both maternity and paternity. Therefore, de novo status cannot be assessed under PS2.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
The variant-specific study reports that ARAF S214C transformed immortalized human airway epithelial cells in a sorafenib-sensitive manner, which is directionally supportive of an oncogenic/damaging effect. However, the available record is an abstract-level description and does not provide sufficient assay-control details, independent replication, quantitative results, or evidence that the assay is validated, reproducible, and robust in a clinical diagnostic laboratory setting. Therefore, the evidence cannot be confirmed as well-established functional evidence for PS3 under the generic ACMG/AMP definition, and no calibrated PS3 strength is assigned.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established.
The governing rule requires significantly increased prevalence in affected individuals versus controls, with an odds ratio or relative risk >5.0 and a confidence interval that excludes 1.0. PMID:24569458 was checked because it was the only variant-specific paper in literature_pass.json: it reports ARAF S214C in one lung adenocarcinoma patient and additional mutations at the residue in a cancer cohort, but it does not provide affected-versus-unaffected/population control counts for this exact variant, so an OR and 95% CI cannot be calculated. No qualifying case-control comparison is available in the supplied evidence.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
PM3 cannot be assessed from the available evidence. The case identifies ARAF NM_001654.5:c.641C>G (p.Ser214Cys), but it provides no established recessive ARAF disorder, no affected-proband observations, no pathogenic allele in the same individual, and no parental or offspring testing establishing trans phase. The required phase and inheritance evidence for PM3 is therefore missing.
For recessive disorders, detected in trans with a pathogenic variant ... Note: This requires testing of parents (or offspring) to determine phase.
The available case materials do not provide a germline proband disease phenotype, family-history assessment, or evidence that the variant was assumed to be de novo without parental confirmation. PM6 cannot be assessed.
Assumed de novo, but without confirmation of paternity and maternity.
The available case materials contain no affected relatives, family pedigree, variant-status results in relatives, or meioses supporting co-segregation. PP1 cannot be assessed.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
The available case evidence does not establish both required gene-level conditions for PP2: a low rate of benign missense variation and missense variants as a common mechanism of disease. Absence of this individual variant from gnomAD and somatic gain-of-function cancer evidence do not establish those gene-wide germline properties.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
The governing rule requires a patient phenotype or family history highly specific for a disease with a single genetic etiology. The supplied case evidence identifies the molecular variant and a somatic lung adenocarcinoma publication, but does not provide a patient phenotype or family history that meets this specificity requirement.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
BS2 cannot be assessed from the available evidence. No healthy adult carrier, homozygote, or hemizygote observation for this variant is reported. Absence from population databases is not evidence that the variant was observed in a healthy adult, and the case evidence does not establish an early-onset, fully penetrant disorder context or provide the required healthy-observation data.
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
No evidence was identified showing that ARAF S214C has no damaging effect on protein function or splicing. The available variant-specific functional report instead describes transformation of immortalized human airway epithelial cells in a sorafenib-sensitive manner, but that finding is not evidence for the BS3 direction. Accordingly, BS3 is not assessed rather than applied or rejected on the basis of the reported oncogenic assay.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
The available case materials contain no affected relatives with reliable phenotype information and no relative genotypes showing that the variant fails to segregate with disease. BS4 cannot be assessed, and no phenocopy or multilocus explanation can be evaluated.
Lack of segregation in affected members of a family.
The available case evidence does not establish that ARAF disease is caused primarily by truncating variants. The identified ARAF S214C report is a somatic missense oncogenic study and cannot establish the variant-spectrum pattern required for BP1.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
BP2 cannot be assessed from the available evidence. The case provides no established fully penetrant dominant ARAF disorder, no pathogenic variant observed in trans with NM_001654.5:c.641C>G, no pathogenic variant observed in cis, and no parental or offspring testing establishing phase. The required allelic relationship is therefore missing.
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
The governing rule requires the variant to be found in a case with an alternate molecular basis for disease. The supplied evidence does not document an individual case in which an alternate molecular cause explains the disease, so BP5 cannot be assessed.
Variant found in a case with an alternate molecular basis for disease.
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_001654.5:c.641C>G in ARAF is a missense substitution predicted to produce NP_001645.1:p.(Ser214Cys). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for ARAF, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_001654.5:c.641C>G in ARAF is a missense substitution predicted to produce NP_001645.1:p.(Ser214Cys). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for ARAF, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_001654.5:c.641C>G in ARAF is a missense substitution predicted to produce NP_001645.1:p.(Ser214Cys). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for ARAF, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_001654.5:c.641C>G in ARAF is a missense substitution predicted to produce NP_001645.1:p.(Ser214Cys). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for ARAF, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in ARAF, mapped onto the exon structure of NM_001654.5. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
Generic ACMG/AMP PP3 is applicable because NM_001654.5:c.641C>G is a missense variant, NP_001645.1:p.(Ser214Cys), and the governing generic path for a missense variant is REVEL only. REVEL is unavailable for this variant, so no calibrated PP3 threshold can be met. The recorded BayesDel score (0.125166) is not usable because no generic ACMG-strength calibration is established for BayesDel; the unavailable SpliceAI result is not an alternative path for a missense PP3 assessment. Therefore PP3 is not met.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent
Generic ACMG/AMP BP4 is applicable because NM_001654.5:c.641C>G is a missense variant, and the governing generic path for a missense variant is REVEL only. REVEL is unavailable, so no calibrated BP4 threshold can be met. The recorded BayesDel score (0.125166) is not usable because no generic ACMG-strength calibration is established for BayesDel; SpliceAI returned no score and is not the applicable path for a missense BP4 assessment. Therefore BP4 is not met.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion.
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_001654.5:c.641C>G in ARAF is a missense substitution predicted to produce NP_001645.1:p.(Ser214Cys). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for ARAF, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI returned NO scores for this variant, so no SpliceAI-based splice prediction is available. This is missing data, NOT evidence of absent splice impact: it must not be used to support BP4 or to argue against PP3/PVS1. Pangolin scores may be present but are not calibrated for PP3/BP4 here. BayesDel score = 0.125166.
1 paper record listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
The ARAF mutations were shown to transform immortalized human airway epithelial cells in a sorafenib-sensitive manner.
PubMed abstract
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The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
This variant is absent from ClinVar.
SpliceAI returned NO scores for this variant, so no SpliceAI-based splice prediction is available. This is missing data, NOT evidence of absent splice impact: it must not be used to support BP4 or to argue against PP3/PVS1. Pangolin scores may be present but are not calibrated for PP3/BP4 here. BayesDel score = 0.125166.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant lies in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant lies in a statistically significant hotspot.