Updates for c.54-589A>G:
2024-10-14 Class updated from VUS3 to likely benign




Variant NM_000492.4:c.54-589A>G


Variant details:
Name NM_000492.4:c.54-589A>G
Protein name NP_000483.3:p.(=)
Genomic name (hg19)     chr7:g.117143718A>G    UCSC    
Genomic name (hg38) chr7:g.117503664A>G    UCSC
#Exon/intron intron 1
Class likely benign
WT sequence CTGCTATGGAGTGAGGAGACAAAAC A TAAGAAAGTTATGATCCTACCCTCA
Mutant sequence CTGCTATGGAGTGAGGAGACAAAAC G TAAGAAAGTTATGATCCTACCCTCA

Other databases:

Not found
Not found		dbSNP
rs34654194







Pathogenicity predictors:

Not found




59 individuals carrying this variant are reported in CFTR-NGS catalogue


16 patients carrying this variant are reported in CFTR-France:

TOTAL NUMBER OF PATIENTS 16
CF 5
CFTR-RD7
  • Bronchiectasis  2
  • CBAVD  2
  • Other  3
Pending (NBS) 4




Color code:   non disease-causing <   likely benign <   VUS <   likely pathogenic <   disease-causing

Detailed genotypes:
Phenotype Patient ID Variant status Additional variants
Pending (NBS) 4787heterozygoteCF-causing- Undef
varying clinical consequence- Undef
Pending (NBS) 5190heterozygoteCF-causing- Undef
VUS3- Undef
varying clinical consequence- Undef
Pending (NBS) 5183heterozygoteCF-causing- Undef
CFTR-RD-causing- Undef
Pending (NBS) 5202heterozygoteCF-causing- Undef
CFTR-RD-causing- Undef
Other 5184heterozygoteVUS3- Undef
CF-causing- Undef
varying clinical consequence- Undef
Other 4800heterozygoteVUS3- Undef
CF-causing- Undef
varying clinical consequence- Undef
Other 4799heterozygoteCF-causing- Undef
varying clinical consequence- Undef
CF 5189heterozygoteCF-causing- Undef
varying clinical consequence- Undef
CF 5186heterozygoteCF-causing- Undef
varying clinical consequence- Undef
CF 5185heterozygoteCF-causing- Undef
CF-causing- Undef
CF 4796heterozygoteVUS3- Undef
CF-causing- Undef
varying clinical consequence- Undef
CF 4791heterozygoteCF-causing- Undef
CF-causing- Undef
CBAVD 5234heterozygoteCFTR-RD-causing- Undef
CF-causing- Undef
CBAVD 5181heterozygoteVUS3- Undef
CF-causing- Undef
Bronchiectasis 5182heterozygoteCF-causing- Undef
varying clinical consequence- Undef
Bronchiectasis 5200heterozygoteCF-causing- Undef
non-CF- Undef


Color code:   non disease-causing <   likely benign <   VUS <   likely pathogenic <   disease-causing



            CFTR variants are clustered into five groups (click here for more details about the classification of variants):
  • CF-causing: when in trans with another CF-causing mutation, will result in CF.
  • CFTR-RD causing: when in trans with a CF-causing mutation, will result in CFTR-related disorders (CFTR-RD) such as chronic pancreatitis, bronchiectasis, CRS-NP (chronic rhinosinusitis with or without nasal polyposis) or CBAVD (congenital absence of vas deferens), according to Bombieri C et al., 2011.
  • Varying clinical consequence: when in trans with another CF-causing mutation, can either result in CF or in a CFTR-RD.
  • Non disease-causing: when in trans with a CF-causing mutation, will not cause CF, nor CFTR-RD.
  • VUS (Variant of unknown clinical significance): unclassified because of insufficient data.



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