The CFTR NM_000492.4:c.3718-2477C>T (NP_000483.3:p.?) intronic variant has not previously been reported in somatic cancers (COSMIC). Experimental evidence: Exact-variant RT-PCR found an 84-bp cryptic exon with an in-frame stop codon and normal CFTR RNA as low as 1% in ileum. Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS). This variant is considered to be Pathogenic by the VCEP (CFTR2; ClinVar ID 7166).
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.CFTR encodes an ATP-binding cassette family protein that functions as a chloride channel, helping regulate salt and water movement across epithelial tissues. Disruption of CFTR causes cystic fibrosis, an inherited disorder affecting the lungs, digestive system, and other organs; CFTR has no established primary role in cancer.
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 supporting strength: exact-variant RT-PCR found an 84-bp cryptic exon with an in-frame stop codon and normal CFTR RNA as low as 1% in ileum.
Met: an affected CF fetus was compound heterozygous for c.3718-2477C>T and F508del, directly documenting the assessed variant in trans with a pathogenic allele.
Met: ClinVar variation 7166 records the exact variant as Pathogenic by the CFTR2 expert panel, meeting the specified PP5 source requirement.
No benign criterion marked as applied in the recorded assessment.
VUS: PS3 supporting, PM3 moderate, and PP5 supporting provide 1 moderate plus 2 supporting criteria, satisfying no generic ACMG pathogenic or benign combination.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 18 / 152,004 alleles. Recorded AF 0.000118418. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 6.37552e-05; MAF= 0.00638%, 2/31370 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00689655; MAF= 0.68966%, 2/290 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.162. Refer to the recorded PP3/BP4 rationale for interpretation.
22 Pathogenic · 2 pathogenic · 1 Likely pathogenic. ClinVar API review status: practice guideline.
No standalone functional evidence summary is recorded in evidence_summary.functional.
This variant has not previously been reported in somatic cancers (COSMIC).
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: 3 met · 9 not met · 7 not assessed · 9 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The phenotype/prevalence group supports PP5 only: the exact variant has a ClinVar CFTR2 expert-panel Pathogenic classification.
PS4 lacks verified exact-variant case-control enrichment, PP4 lacks sufficient patient phenotype detail, BP5 lacks an alternate molecular diagnosis, and BP6 lacks a benign expert-panel assertion.
Generic ACMG/AMP rules govern because no VCEP covers CFTR in this case.
The variant is intronic, so PP3 and BP4 were evaluated through SpliceAI only; BP7 is outside scope because it applies only to synonymous variants.
The SpliceAI max delta of 0.162 is below the PP3 supporting cutoff of 0.2 but above the BP4 supporting cutoff of 0.1.
Population evidence supports none of the four requested criteria: BA1, BS1, BS2, and PM2 are not met.
The decisive population result is gnomAD v4.1 grpmax FAF=0.00016885, which is below the benign thresholds for BA1 and BS1 but above the supplied PM2 cutoff.
No homozygotes are observed in gnomAD v2.1 or v4.1, and no healthy-adult homozygote is documented.
No criteria match.
PS3 is met at supporting strength. PMID:10351951 directly studied the exact CFTR variant, historically reported as 3849 + 10 kb C→T, in fetal tissues using semiquantitative nondifferential and differential RT-PCR. The assay demonstrated insertion of an 84-bp cryptic exon containing an in-frame stop codon and markedly reduced correctly spliced CFTR RNA, with normal transcript proportions of 26% in lung, 17% in trachea, 19% in colon, 2% in pancreas, and 1% in ileum. The concordant aberrant splicing and organ pathology support a damaging effect on CFTR RNA processing. Supporting rather than stronger functional evidence is assigned because this is a single fetal-tissue study, not an independently replicated, clinically validated diagnostic assay, and the available extract does not establish a full control/replication framework.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
PM3 is met for this recessive CFTR disorder. PMID:10351951 reports a 22-week CF fetus compound heterozygous for 3849 + 10 kb C→T, corresponding to NM_000492.4:c.3718-2477C>T, and F508del. The explicit compound-heterozygous observation establishes the alleles were in trans, and the affected fetal CF context supports the other allele as pathogenic for this PM3 observation.
PM3: For recessive disorders, detected in trans with a pathogenic variant...Note: This requires testing of parents (or offspring) to determine phase.
Expert panel CFTR2 classified as Pathogenic.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
No qualifying case-control comparison was verified for NM_000492.4:c.3718-2477C>T. The literature_pass.json packet's ai_classified_papers contains no paper classified as PS4; the PS4 candidate PMID:15371902 was checked in paper_extracts.json and does not mention this exact variant, and no affected-control counts, case frequency with a matched-ancestry control frequency, OR/RR, or confidence interval were reported for this variant. Therefore the required enrichment threshold cannot be met.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: 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.
PM2 is not met under the supplied generic SVI threshold. The variant is present in the applicable all-comers gnomAD v4.1 dataset at AF=0.000118418 (18/152004 alleles), with grpmax FAF=0.00016885; both exceed the PM2 supporting cutoff of <=0.0001. There is no VCEP rule requiring a non-cancer or exome-only subset, so the all-comers result is the governing default. gnomAD v2.1 is lower at AF=0.0000637552, but the current v4.1 filtering frequency does not satisfy PM2.
PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868) ... PM2: Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Scope was settled first under the generic rule: this is an intronic variant (NM_000492.4:c.3718-2477C>T; protein consequence p.?), so PP3 uses the SpliceAI path only; REVEL is not applicable and is not used. SpliceAI max delta is 0.162, below the generic PP3 supporting threshold of >=0.2 and therefore also below the moderate threshold of >=0.5. The result does not meet PP3. The threshold is the published SpliceAI recommended cutoff from Jaganathan et al. 2019 (PMID:30661751).
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
BA1 is not met. The applicable all-comers gnomAD v4.1 result has grpmax FAF=0.00016885, far below the generic stand-alone threshold of 0.05. The highest observed subpopulation point estimate is Ashkenazi Jewish AF=0.00172911 from 6/3470 alleles, but the point estimate is not the filtering allele frequency and does not support BA1; the qualifying population has at least 2000 observed alleles, while the reported grpmax FAF remains below threshold. gnomAD v2.1 also does not support BA1: its Ashkenazi Jewish point estimate is 2/290, below the required 2000 observed alleles, and no grpmax FAF is reported. The variant has a CFTR2 expert-panel Pathogenic ClinVar classification, so the low FAF and pathogenic consensus do not justify a stand-alone benign call.
BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868) ... BA1: Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
BS1 is not met. The applicable all-comers gnomAD v4.1 filtering frequency is grpmax FAF=0.00016885, below the generic default threshold of 0.01 for an allele frequency greater than expected for the disorder. The highest observed Ashkenazi Jewish point estimate, AF=0.00172911 from 6/3470 alleles, must not replace grpmax FAF. No governing VCEP or per-gene maximum-credible-frequency calculation is available; therefore the supplied generic default applies. The CFTR2 expert-panel Pathogenic classification and the frequency well below 1% provide no population-based support for BS1.
BS1: Allele frequency is greater than expected for the disorder. ... BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)
BS2 is not met. gnomAD v4.1 reports 0 homozygotes among 18 observed alleles, and gnomAD v2.1 reports 0 homozygotes among 2 observed alleles. No evidence identifies a healthy adult who is homozygous for this autosomal-recessive CFTR variant; population allele observations alone do not establish the required healthy-adult observation.
BS2: 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.
BP2 is not met. The available observation is compound heterozygosity, indicating the assessed variant is in trans with F508del in an affected CF fetus. BP2 requires an in-trans observation in a fully penetrant dominant gene/disorder or an in-cis observation in any inheritance pattern; neither qualifying BP2 configuration is documented.
BP2: 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.
Scope was settled first under the generic rule: this is an intronic variant (NM_000492.4:c.3718-2477C>T; protein consequence p.?), so BP4 uses the SpliceAI path only; REVEL is not applicable and is not used. SpliceAI max delta is 0.162, above the generic BP4 supporting threshold of <=0.1, so the available prediction does not support no splice impact. The result does not meet BP4. The threshold is the published SpliceAI recommended cutoff from Jaganathan et al. 2019 (PMID:30661751).
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
The exact-variant ClinVar expert-panel record supports Pathogenic classification by CFTR2, not Benign or Likely benign. No exact-variant ClinVar expert-panel benign assertion was identified, so the specified prerequisite for BP6 is absent.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The available evidence documents a CFTR intronic variant in disease-related literature but does not document a de novo occurrence in a patient, confirmed maternity and paternity, or absence of family history. Therefore, the PS2 requirements cannot be assessed.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
The available evidence does not describe an assumed de novo occurrence for this variant in a patient. It also does not provide parental testing information that would support an unconfirmed de novo interpretation. Therefore, PM6 cannot be assessed.
Assumed de novo, but without confirmation of paternity and maternity.
The available evidence does not report affected family members carrying this variant, unaffected relatives lacking it, or the number of informative meioses. Consequently, co-segregation and any possible increased strength cannot be assessed.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... Note: May be used as stronger evidence with increasing segregation data.
The supplied case evidence does not provide a sufficiently detailed patient phenotype or family history for this specific patient. Without phenotype features that are highly specific for cystic fibrosis or another single-gene CFTR-related disease, PP4 cannot be adjudicated.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
No evidence was identified showing that this exact variant has no damaging effect on CFTR protein function or splicing. The available exact-variant functional study instead reports aberrant splicing and reduced correctly spliced CFTR RNA, but it cannot be used to establish BS3.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
The available evidence does not identify affected family members who lack this variant, nor does it provide a pedigree sufficient to evaluate phenocopies or alternative pathogenic variants. Lack of segregation therefore cannot be assessed.
Lack of segregation in affected members of a family. ... Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, fu
No case-level evidence in the supplied materials documents that this variant occurred in a patient with an alternate molecular basis for disease. The available ClinVar record concerns classification of this variant and does not establish an alternate molecular diagnosis in a case.
Variant found in a case with an alternate molecular basis for disease.
NM_000492.4:c.3718-2477C>T is a deep-intronic C>T SNV in CFTR intron 19/exon annotation 22i, not a nonsense, frameshift, initiation-codon, canonical +/-1 or 2 splice-site, or single/multi-exon deletion variant. The transcript consequence is NP_000483.3:p.? and the variant assessment records canonical_splice_consensus=false. Variant-specific RNA evidence shows aberrant splicing with insertion of an 84-bp cryptic exon containing an in-frame stop codon, but that experimentally observed consequence does not change the variant's location/type outside the generic PVS1 null-variant categories named in the rule. Therefore PVS1 is not applicable under the supplied generic ACMG/AMP definition, despite CFTR loss of function being a known disease mechanism.
Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease.
PS1 is not applicable because NM_000492.4:c.3718-2477C>T is a deep-intronic splice variant with protein consequence NP_000483.3:p.? rather than an amino-acid substitution. The reviewed variant-specific study describes insertion of an 84-bp cryptic exon containing an in-frame stop codon, so there is no affected amino-acid change for same-amino-acid comparison.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
PM1 is not applicable because the variant is deep intronic, has no assigned amino-acid residue (NP_000483.3:p.?), and therefore cannot be located at a protein mutational hotspot or critical functional domain. No CFTR VCEP domain table is present, and no residue-based domain assessment can be performed for this splice variant.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
NM_000492.4:c.3718-2477C>T is a deep-intronic C>T SNV with NP_000483.3:p.? rather than a coding in-frame deletion, coding in-frame insertion, or stop-loss variant. Although PMID:10351951 reports an 84-bp cryptic exon inserted through aberrant splicing, the underlying variant is not itself an in-frame coding indel and no stop-loss protein consequence is assigned. It therefore lies outside the variant types named by the generic PM4 rule.
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.
PM5 is not applicable because this is a deep-intronic splice variant with protein consequence p.? and no amino-acid residue at which an alternate missense change could be compared. The variant-specific study demonstrates aberrant splicing with an 84-bp cryptic exon and an in-frame stop codon.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
PP2 is not applicable because the criterion is limited to missense variants, whereas NM_000492.4:c.3718-2477C>T is a deep-intronic splice variant with protein consequence p.?. The reviewed functional study shows aberrant splicing rather than a missense mechanism.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
BP1 is not applicable because the criterion is limited to missense variants, whereas NM_000492.4:c.3718-2477C>T is a deep-intronic splice variant with protein consequence p.?. Its documented mechanism is aberrant splicing with cryptic-exon insertion, not a missense change.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
NM_000492.4:c.3718-2477C>T is a deep-intronic C>T SNV, not an in-frame deletion or insertion. The available variant-specific evidence describes aberrant splicing with an 84-bp cryptic exon, not a repetitive-region coding indel, and no repetitive region with no known function is established for this variant. Because the variant is outside the in-frame deletion/insertion type named by BP3, BP3 is not applicable.
In frame-deletions/insertions in a repetitive region without a known function.
BP7 is limited to synonymous variants. NM_000492.4:c.3718-2477C>T is an intronic variant with protein consequence p.?, not a synonymous coding variant, so BP7 is outside its governing scope and is not applicable.
A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.
Every interpreted variant in CFTR, mapped onto the exon structure of NM_000492.4. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Ashkenazi Jewish6 / 3,470 | 0.0017 |
| South Asian3 / 4,828 | 0.00062 |
| Remaining individuals1 / 2,086 | 0.00048 |
| Admixed American2 / 15,262 | 0.00013 |
| European (non-Finnish)6 / 67,970 | 8.8e-05 |
| Ashkenazi Jewish2 / 290 | 0.0069 |
This variant is present in gnomAD v4.1 (AF= 0.000118418; MAF= 0.01184%, 18/152004 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00172911; MAF= 0.17291%, 6/3470 alleles, homozygotes = 0); grpmax FAF= 0.00016885.
This variant is present in gnomAD v2.1 (AF= 6.37552e-05; MAF= 0.00638%, 2/31370 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00689655; MAF= 0.68966%, 2/290 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
Scope was settled first under the generic rule: this is an intronic variant (NM_000492.4:c.3718-2477C>T; protein consequence p.?), so PP3 uses the SpliceAI path only; REVEL is not applicable and is not used. SpliceAI max delta is 0.162, below the generic PP3 supporting threshold of >=0.2 and therefore also below the moderate threshold of >=0.5. The result does not meet PP3. The threshold is the published SpliceAI recommended cutoff from Jaganathan et al. 2019 (PMID:30661751).
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
Scope was settled first under the generic rule: this is an intronic variant (NM_000492.4:c.3718-2477C>T; protein consequence p.?), so BP4 uses the SpliceAI path only; REVEL is not applicable and is not used. SpliceAI max delta is 0.162, above the generic BP4 supporting threshold of <=0.1, so the available prediction does not support no splice impact. The result does not meet BP4. The threshold is the published SpliceAI recommended cutoff from Jaganathan et al. 2019 (PMID:30661751).
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
BP7 is limited to synonymous variants. NM_000492.4:c.3718-2477C>T is an intronic variant with protein consequence p.?, not a synonymous coding variant, so BP7 is outside its governing scope and is not applicable.
A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.16).
9 paper records listed. 1 cited in the classification.
This mutation creates a partially active splice site in intron 19 of the CFTR gene, which can lead to the insertion of a new 84-bp “exon,” harboring an in-frame stop codon, between exons 19 and 20
Location Results and Discussion; Table 1
Context Case study of tissues from a 22-week aborted CF fetus compound heterozygous for 3849 + 10 kb C→T and F508del; semiquantitative nondifferential and differential RT-PCR measured correctly and aberrantly spliced CFTR transcripts in lung, trachea, colon, pancreas, ileum, and heart, with histopathologic analysis.
The mutation/variant I148T occurs at rates 50 to 100 times higher than in the general population being tested for carrier status than in patients. It was shown that CFTR genes bearing I148T in CF patients have a second mutation termed 3199del6.
Discussion of general-population prevalence and interpretation of CFTR variants
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 0.000118418; MAF= 0.01184%, 18/152004 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00172911; MAF= 0.17291%, 6/3470 alleles, homozygotes = 0); grpmax FAF= 0.00016885.
This variant is present in gnomAD v2.1 (AF= 6.37552e-05; MAF= 0.00638%, 2/31370 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.00689655; MAF= 0.68966%, 2/290 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Pathogenic (22 clinical laboratories) and as pathogenic (2 clinical laboratories) and as Likely pathogenic (1 clinical laboratory) and as Pathogenic by CFTR2 (expert panel). (ClinVarID = 7166)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.16).
This variant has not previously been reported in somatic cancers (COSMIC).