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This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
CFTR
Final classification
VUS
CFTR c.2723C>G · p.Thr908Ser
CFTR

NM_000492.4:c.2723C>G (p.Thr908Ser) is a missense variant in exon 17 of CFTR, a gene in which both missense and loss-of-function variants are established disease mechanisms for cystic fibrosis and CFTR-related disorders.

Gene
CFTR
Transcript
NM_000492.4
HGVS · transcript:coding
NM_000492.4:c.2723C>G
Consequence
N/A
GRCh38
chr7:117603597 C>G
GRCh37
chr7:117243651 C>G
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
CFTR c.2723C>G

NM_000492.4:c.2723C>G (p.Thr908Ser) is a missense variant in exon 17 of CFTR, a gene in which both missense and loss-of-function variants are established disease mechanisms for cystic fibrosis and CFTR-related disorders.1 This variant is present in gnomAD v4.1 at an extremely low allele frequency (2.48e-6; 4/1,613,954 alleles, 0 homozygotes) and is absent from gnomAD v2.1 and gnomAD-Canada v1.0, meeting PM2 at supporting strength.2 Computational evidence is conflicting: REVEL score 0.557 is borderline, BayesDel score -0.037 is neutral, and SpliceAI max delta score 0.02 predicts no splicing impact; thus PP3 is not met and BP4 is not met.3 ClinVar classifies this variant as Uncertain significance based on a single clinical laboratory submission (GeneDx, SCV002549489, criteria provided, single submitter). No functional studies, segregation data, de novo observations, or case-control data were identified.4 With only one supporting pathogenic criterion (PM2) and no benign criteria met, the evidence is insufficient to meet thresholds for Likely Pathogenic or Likely Benign classification. The variant is classified as Uncertain significance per ACMG/AMP 2015 guidelines.5

PM2 VUS
1 pvs1_gene_context
3 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_000492.4 · variants mapped to exon structure
CFTR NM_000492.4
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 2.47839e-06; MAF= 0.00025%, 4/1613954 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.39026e-06; MAF= 0.00034%, 4/1179850 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00025% · 4 / 1,613,954
      0 hom · FAF 7.9e-05%
      European (non-Finnish)
      4 / 1,179,850
      0.00034%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 1697071)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.557. BayesDel score = -0.0370847.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots