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NM_000492.4(CFTR):c.1766+5G>T

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel
Submissions:
9 (Most recent: Sep 2, 2021)
Last evaluated:
Mar 17, 2017
Accession:
VCV000048685.14
Variation ID:
48685
Description:
single nucleotide variant
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NM_000492.4(CFTR):c.1766+5G>T

Allele ID
57847
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q31.2
Genomic location
7: 117590444 (GRCh38) GRCh38 UCSC
7: 117230498 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_663:g.129661G>T
LRG_663t1:c.1766+5G>T
NM_000492.3:c.1766+5G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:117590443:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00004
The Genome Aggregation Database (gnomAD) 0.00006
Links
ClinGen: CA326663
Genetic Testing Registry (GTR): GTR000074114
Genetic Testing Registry (GTR): GTR000576392
dbSNP: rs121908796
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 7 reviewed by expert panel Mar 17, 2017 RCV000046468.11
Pathogenic 1 criteria provided, single submitter - RCV001004274.1
Pathogenic 1 no assertion criteria provided - RCV001528994.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CFTR - - GRCh38
GRCh37
1954 2699

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Mar 17, 2017)
reviewed by expert panel
Method: research
Cystic fibrosis
Allele origin: germline
CFTR2
Study: CFTR2
Accession: SCV000677595.1
Submitted: (Jun 29, 2017)
Evidence details
Other databases
https://cftr2.org
Pathogenic
(Oct 16, 2019)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV001167246.1
Submitted: (Nov 14, 2019)
Evidence details
Comment:
Disease-causing CFTR variant. See www.CFTR2.org for phenotype information.
Pathogenic
(Aug 06, 2020)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
Allele origin: germline
Invitae
Accession: SCV000074481.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (7)
Comment:
This sequence change falls in intron 13 of the CFTR gene. It does not directly change the encoded amino acid sequence of the CFTR protein, … (more)
Pathogenic
(Jul 08, 2016)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696872.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: The CFTR c.1766+5G>T variant involves the alteration of a conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant, … (more)
Likely pathogenic
(Feb 10, 2017)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000712857.1
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (2)
Comment:
The c.1766+5G>T (NM_000492.3 c.1766+5G>T) variant in CFTR has been reported in 1 homozygous and 3 compound heterozygous Asian individuals with clinical features of cystic fibrosis … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Congenital bilateral aplasia of vas deferens from CFTR mutation
Cystic fibrosis
Allele origin: germline
Baylor Genetics
Accession: SCV001163150.1
Submitted: (Sep 27, 2019)
Evidence details
Pathogenic
(Jan 29, 2018)
criteria provided, single submitter
Method: curation
cystic fibrosis
Allele origin: germline
CFTR-France
Accession: SCV001169435.1
Submitted: (Sep 16, 2019)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(Dec 04, 2019)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
Allele origin: unknown
Myriad Women's Health, Inc.
Accession: SCV001194057.2
Submitted: (Jun 18, 2020)
Evidence details
Publications
PubMed (8)
Comment:
NM_000492.3(CFTR):c.1766+5G>T(aka 1898+5G>T) is classified as likely pathogenic in the context of cystic fibrosis. Sources cited for classification include the following: PMID 23089694, 8213163, 25580864, 16202790, … (more)
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001741691.3
Submitted: (Sep 02, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
CFTR-France, a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants. Claustres M Human mutation 2017 PMID: 28603918
Clinical Phenotypes and Genotypic Spectrum of Cystic Fibrosis in Chinese Children. Shen Y The Journal of pediatrics 2016 PMID: 26826884
Characterization of gene mutations and phenotypes of cystic fibrosis in Chinese patients. Liu Y Respirology (Carlton, Vic.) 2015 PMID: 25580864
A classification model relative to splicing for variants of unknown clinical significance: application to the CFTR gene. Raynal C Human mutation 2013 PMID: 23381846
Acute appendicitis mimicking intestinal obstruction in a patient with cystic fibrosis. Chen CH Journal of the Formosan Medical Association = Taiwan yi zhi 2012 PMID: 23089694
Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. Castellani C Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society 2008 PMID: 18456578
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Two-tiered immunoreactive trypsinogen-based newborn screening for cystic fibrosis in Colorado: screening efficacy and diagnostic outcomes. Sontag MK The Journal of pediatrics 2005 PMID: 16202790
Detection of novel CFTR mutations in Taiwanese cystic fibrosis patients. Alper OM Journal of the Formosan Medical Association = Taiwan yi zhi 2003 PMID: 12874665
Novel cystic fibrosis mutation (2215insG) in two adolescent Taiwanese siblings. Wu CL Journal of the Formosan Medical Association = Taiwan yi zhi 2000 PMID: 10925568
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098
Skipping of exon 12 as a consequence of a point mutation (1898 + 5G-->T) in the cystic fibrosis transmembrane conductance regulator gene found in a consanguineous Chinese family. Zielenski J Clinical genetics 1995 PMID: 7543385
Cystic fibrosis in two Chinese infants in Taiwan. Wang MC Zhonghua Minguo xiao er ke yi xue hui za zhi [Journal]. Zhonghua Minguo xiao er ke yi xue hui 1993 PMID: 8213163
https://cftr2.org - - - -

Text-mined citations for rs121908796...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 07, 2021