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NM_000492.4(CFTR):c.1251C>A (p.Asn417Lys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Nov 4, 2021)
Last evaluated:
Nov 3, 2021
Accession:
VCV000193592.8
Variation ID:
193592
Description:
single nucleotide variant
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NM_000492.4(CFTR):c.1251C>A (p.Asn417Lys)

Allele ID
190755
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q31.2
Genomic location
7: 117548682 (GRCh38) GRCh38 UCSC
7: 117188736 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.117188736C>A
NM_000492.3:c.1251C>A NP_000483.3:p.Asn417Lys missense
LRG_663:g.87899C>A
... more HGVS
Protein change
N417K
Other names
-
Canonical SPDI
NC_000007.14:117548681:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.01885
Links
ClinGen: CA200678
dbSNP: rs4727853
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jul 22, 2021 RCV000366455.6
Benign 1 criteria provided, single submitter Mar 21, 2015 RCV000173697.1
CFTR-related disorders
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001095146.1
Uncertain significance 1 criteria provided, single submitter Nov 3, 2021 RCV001762396.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Aug 22, 2017 RCV000224343.4
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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
CFTR-AS1 - - - GRCh38 - 286

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 28, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281114.1
Submitted: (May 19, 2016)
Evidence details
Benign
(Mar 21, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000224841.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Aug 22, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696832.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: The CFTR c.1251C>A (p.Asn417Lys) variant involves the alteration of a non-conserved nucleotide. 3/5 in silico tools predict a benign outcome for this variant. … (more)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
CFTR-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000466511.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Nov 06, 2020)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
Allele origin: germline
Invitae
Accession: SCV000562317.6
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Cystic fibrosis
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001822043.1
Submitted: (Sep 01, 2021)
Evidence details
Uncertain significance
(Nov 03, 2021)
criteria provided, single submitter
Method: clinical testing
Hereditary pancreatitis
Allele origin: germline
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002009135.1
Submitted: (Nov 04, 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
Defects in myosin VB are associated with a spectrum of previously undiagnosed low γ-glutamyltransferase cholestasis. Qiu YL Hepatology (Baltimore, Md.) 2017 PMID: 28027573
A novel computational and structural analysis of nsSNPs in CFTR gene. George Priya Doss C Genomic medicine 2008 PMID: 18716917
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CFTR - - - -

Text-mined citations for rs4727853...

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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 06, 2021