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NM_000492.4(CFTR):c.273+3A>C

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel
Submissions:
4 (Most recent: Jun 18, 2020)
Last evaluated:
Mar 17, 2017
Accession:
VCV000035846.5
Variation ID:
35846
Description:
single nucleotide variant
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NM_000492.4(CFTR):c.273+3A>C

Allele ID
44510
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q31.2
Genomic location
7: 117509145 (GRCh38) GRCh38 UCSC
7: 117149199 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_663:g.48362A>C
LRG_663t1:c.273+3A>C
NC_000007.14:g.117509145A>C
... more HGVS
Protein change
-
Other names
405+3A->C
Canonical SPDI
NC_000007.14:117509144:A:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
dbSNP: rs74467662
ClinGen: CA325701
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 reviewed by expert panel Mar 17, 2017 RCV000029501.7
Pathogenic 1 criteria provided, single submitter - RCV001004421.1
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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
1972 2727

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: SCV000245989.2
Submitted: (Jun 29, 2017)
Evidence details
Other databases
https://cftr2.org
Likely pathogenic
(Jun 28, 2019)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000052152.3
Submitted: (Sep 24, 2019)
Evidence details
Publications
PubMed (12)
Comment:
Variant summary: CFTR c.273+3A>C alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (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: SCV001163465.1
Submitted: (Sep 27, 2019)
Evidence details
Likely pathogenic
(Dec 04, 2019)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
Allele origin: unknown
Myriad Women's Health, Inc.
Accession: SCV001193953.2
Submitted: (Jun 18, 2020)
Evidence details
Publications
PubMed (2)
Comment:
NM_000492.3(CFTR):c.273+3A>C(aka 405+3A>C) is classified as likely pathogenic in the context of cystic fibrosis. Sources cited for classification include the following: PMID 9150159 and 11388756. Classification … (more)

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
The Spectrum of CFTR Variants in Nonwhite Cystic Fibrosis Patients: Implications for Molecular Diagnostic Testing. Schrijver I The Journal of molecular diagnostics : JMD 2016 PMID: 26708955
An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals. Lazarin GA Genetics in medicine : official journal of the American College of Medical Genetics 2013 PMID: 22975760
Mutation nomenclature in practice: findings and recommendations from the cystic fibrosis external quality assessment scheme. Berwouts S Human mutation 2011 PMID: 21796730
The suitability of matrix assisted laser desorption/ionization time of flight mass spectrometry in a laboratory developed test using cystic fibrosis carrier screening as a model. Farkas DH The Journal of molecular diagnostics : JMD 2010 PMID: 20616359
Characterization of publicly available lymphoblastoid cell lines for disease-associated mutations in 11 genes. Bernacki SH Clinical chemistry 2005 PMID: 16244288
Genotyping microarray for the detection of more than 200 CFTR mutations in ethnically diverse populations. Schrijver I The Journal of molecular diagnostics : JMD 2005 PMID: 16049310
Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. Watson MS Genetics in medicine : official journal of the American College of Medical Genetics 2004 PMID: 15371902
Novel CFTR mutations in black cystic fibrosis patients. Feuillet-Fieux MN Clinical genetics 2004 PMID: 15025720
Development and evaluation of a PCR-based, line probe assay for the detection of 58 alleles in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Wang X Clinical chemistry 2002 PMID: 12089190
Genetic markers of male infertility: Y chromosome microdeletions and cystic fibrosis transmembrane conductance gene mutations. Sertić J Croatian medical journal 2001 PMID: 11471192
Improved detection of cystic fibrosis mutations in the heterogeneous U.S. population using an expanded, pan-ethnic mutation panel. Heim RA Genetics in medicine : official journal of the American College of Medical Genetics 2001 PMID: 11388756
Cystic fibrosis carrier frequencies in populations of African origin. Padoa C Journal of medical genetics 1999 PMID: 9950364
Identification of common cystic fibrosis mutations in African-Americans with cystic fibrosis increases the detection rate to 75%. Macek M Jr American journal of human genetics 1997 PMID: 9150159
https://cftr2.org - - - -

Text-mined citations for rs74467662...

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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 Nov 27, 2021