Variant NM_000492.4:c.2989-1G>A


Variant details:
Name NM_000492.4:c.2989-1G>A
Protein name NP_000483.3:p.(=)
Genomic name (hg19) chr7:g.117250572G>A    UCSC    
#Exon/intron intron 18
Legacy Name 3121-1G>A
Class disease-causing
Subclass CF-causing
WT sequence CCAACATGTTTTCTTTGATCTTACA G TTGTTATTAATTGTGATTGGAGCTA
Mutant sequence CCAACATGTTTTCTTTGATCTTACA A TTGTTATTAATTGTGATTGGAGCTA

Other databases:
dbSNP
rs397508470







Pathogenicity predictors:

Not found





No patient found in CFTR-NGS catalogue


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

TOTAL NUMBER OF PATIENTS 12
Asymptomatic compound heterozygote 2
CF 7
CFTR-RD2
  • CBAVD  1
  • Pancreatitis  1
Fetal bowel anomalies 1




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

Detailed genotypes:
Phenotype Patient ID Variant status Additional variants
Asymptomatic compound heterozygote 4691heterozygoteVUS1 - Trans
Asymptomatic compound heterozygote 4289heterozygote
CF 2399heterozygoteCF-causing- Undef
CF 2384heterozygoteCF-causing- Undef
CF 2379heterozygoteCF-causing- Undef
CF 2170heterozygoteCF-causing- Undef
CF 1825heterozygoteCF-causing- Undef
CF 651heterozygoteCF-causing - Trans
CF 4290heterozygoteCF-causing - Trans
Pancreatitis 5455heterozygoteCFTR-RD-causing- Undef
CBAVD 6245heterozygotevarying clinical consequence- Undef
Fetal bowel anomalies 4020heterozygoteCF-causing- Undef


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



            CFTR variants are clustered into five groups:
  • 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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