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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 applied · 20 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is present in gnomAD v4.1 at an extremely low allele frequency (2.48e-6; 4/1,613,954 alleles, 0 homozygotes), absent from gnomAD v2.1, and absent from gnomAD-Canada v1.0. The frequency is well below the 0.1% threshold for PM2.
gnomAD v4.1: AF=2.48e-64/1613
Assessed · not applied
Pathogenic
PS1 No pathogenic variant at the same codon (Thr908) with the same amino acid change resulting from a different nucleotide substitution has been identified.
PS2 No de novo observation with confirmed maternity and paternity is available for this variant.
PS3 No well-established in vitro or in vivo functional studies demonstrating a damaging effect were identified for this variant.
PS4 No case-control data demonstrating significantly increased prevalence in affected individuals versus controls is available.
PM1 The variant is not located in a statistically significant mutational hotspot.
PM6 No de novo observation (without confirmed maternity and paternity) is available for this variant.
PP1 No co-segregation data in affected family members is available.
PP2 HCI prior is not available for CFTR; gene-specific constraint metrics cannot be evaluated.
PP3 Multiple lines of computational evidence are conflicting and do not support a deleterious effect.
PP4 No patient phenotype or family history data is available to assess disease specificity.
PP5 ClinVar classifies this variant as Uncertain significance (1 submitter, criteria provided, single submitter).
Benign
BA1 The maximum population allele frequency for this variant is 2.48e-6 (gnomAD v4.1), which is far below the 1% threshold for BA1.
BS1 The maximum population allele frequency for this variant is 2.48e-6 (gnomAD v4.1), which is far below the 0.3% threshold for BS1.
BS2 No homozygotes have been observed in gnomAD (0/1,613,954 alleles).
BS3 No well-established in vitro or in vivo functional studies demonstrating no damaging effect were identified for this variant.
BS4 No segregation data in affected family members is available.
BP2 No data on this variant observed in trans with a pathogenic variant or in cis with a pathogenic variant is available.
BP4 Multiple lines of computational evidence do not agree on a lack of impact.
BP5 No data on this variant found in a case with an alternate molecular basis for disease is available.
BP6 ClinVar classifies this variant as Uncertain significance (1 submitter).
N/A · 7 PVS1 · PM3 · PM4 · PM5 · BP1 · BP3 · BP7
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