NM_000492.4(CFTR):c.3874-2A>G AND Cystic fibrosis

Clinical significance:Likely pathogenic (Last evaluated: Mar 30, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000589248.1

Allele description [Variation Report for NM_000492.4(CFTR):c.3874-2A>G]

NM_000492.4(CFTR):c.3874-2A>G

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.3874-2A>G
HGVS:
  • NC_000007.14:g.117652840A>G
  • NG_016465.4:g.192057A>G
  • NM_000492.4:c.3874-2A>GMANE SELECT
  • LRG_663t1:c.3874-2A>G
  • LRG_663:g.192057A>G
  • NC_000007.13:g.117292894A>G
  • NM_000492.3:c.3874-2A>G
Links:
dbSNP: rs1554396384
NCBI 1000 Genomes Browser:
rs1554396384
Molecular consequence:
  • NM_000492.4:c.3874-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV000696996Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely pathogenic
(Mar 30, 2017)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696996.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The c.3874-2A>G in CFTR gene is a splice-site variant that alters a highly conserved nucleotide. 5/5 in silico tools via Alamut predict the loss of canonical acceptor sequence, although these predictions are yet to be confirmed by the functional studies. The variant is absent from control datasets of ExAC and gnomAD (0/114018 and 0/241528 chrs tested, respectively). Lastly, the variant has not, to our knowledge, been reported in affected individuals via published reports or cited by reputable databases/diagnostic centers. Taken together, the variant was classified as Likely Pathogenic.

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

Last Updated: Nov 27, 2021

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