NM_000492.4(CFTR):c.3469-20T>C AND Cystic fibrosis

Clinical significance:Conflicting interpretations of pathogenicity, Benign(2);Uncertain significance(1) (Last evaluated: Dec 8, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000007649.9

Allele description [Variation Report for NM_000492.4(CFTR):c.3469-20T>C]

NM_000492.4(CFTR):c.3469-20T>C

Gene:
CFTR:CF transmembrane conductance regulator [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q31.2
Genomic location:
Preferred name:
NM_000492.4(CFTR):c.3469-20T>C
HGVS:
  • NC_000007.14:g.117627502T>C
  • NG_016465.4:g.166719T>C
  • NM_000492.4:c.3469-20T>CMANE SELECT
  • LRG_663t1:c.3469-20T>C
  • LRG_663:g.166719T>C
  • NC_000007.13:g.117267556T>C
  • NG_016465.3:g.166719T>C
  • NM_000492.3:c.3469-20T>C
Nucleotide change:
3601, T-C, -20
Links:
OMIM: 602421.0126; dbSNP: rs373002889
NCBI 1000 Genomes Browser:
rs373002889
Molecular consequence:
  • NM_000492.4:c.3469-20T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Cystic fibrosis (CF)
Synonyms:
Mucoviscidosis
Identifiers:
MONDO: MONDO:0009061; MedGen: C0010674; Orphanet: 586; OMIM: 219700

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000027850OMIMno assertion criteria providedPathogenic
(Jul 17, 2000)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV001137493Mendelicscriteria provided, single submitter
Uncertain significance
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV001435188Broad Institute Rare Disease Group, Broad Institutecriteria provided, single submitter
Benigngermlineresearch

PubMed (4)
[See all records that cite these PMIDs]

SCV001731520Invitaecriteria provided, single submitter
Benign
(Dec 8, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedresearch
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Is the spectrum of mutations in Indian patients with cystic fibrosis different?

Kabra M, Kabra SK, Ghosh M, Khanna A, Arora S, Menon PS, Verma IC, Wallace A.

Am J Med Genet. 2000 Jul 17;93(2):161-3. No abstract available. Erratum in: Am J Med Genet 2000 Dec 11;95(4):410.

PubMed [citation]
PMID:
10869121

Idiopathic chronic pancreatitis in India: phenotypic characterisation and strong genetic susceptibility due to SPINK1 and CFTR gene mutations.

Midha S, Khajuria R, Shastri S, Kabra M, Garg PK.

Gut. 2010 Jun;59(6):800-7. doi: 10.1136/gut.2009.191239.

PubMed [citation]
PMID:
20551465
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000027850.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 2 Indian patients with cystic fibrosis (CF; 219700), Kabra et al. (2000) identified a T-to-C change at position -20 from nucleotide 3601 of the CFTR gene.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV001137493.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Broad Institute Rare Disease Group, Broad Institute, SCV001435188.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (4)

Description

The heterozygous c.3469-20T>C variant in CFTR has been reported in at least 3 individuals with cystic fibrosis without another variant identified in the gene (PMID: 10869121, 20551465, 21520337), and has been identified in >1% of South Asian chromosomes and 7 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for autosomal recessive cystic fibrosis.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001731520.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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