NM_001042492.3(NF1):c.1721+3A>G AND not provided

Clinical significance:Pathogenic (Last evaluated: Oct 7, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000992429.2

Allele description [Variation Report for NM_001042492.3(NF1):c.1721+3A>G]

NM_001042492.3(NF1):c.1721+3A>G

Gene:
NF1:neurofibromin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q11.2
Genomic location:
Preferred name:
NM_001042492.3(NF1):c.1721+3A>G
HGVS:
  • NC_000017.11:g.31221932A>G
  • NG_009018.1:g.131956A>G
  • NM_000267.3:c.1721+3A>G
  • NM_001042492.3:c.1721+3A>GMANE SELECT
  • NM_001128147.3:c.1724A>G
  • NP_001121619.1:p.Tyr575Cys
  • LRG_214t1:c.1721+3A>G
  • LRG_214t2:c.1721+3A>G
  • LRG_214:g.131956A>G
  • NC_000017.10:g.29548950A>G
  • NM_001042492.2:c.1721+3A>G
Protein change:
Y575C
Links:
dbSNP: rs1057518904
NCBI 1000 Genomes Browser:
rs1057518904
Molecular consequence:
  • NM_000267.3:c.1721+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001042492.3:c.1721+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001128147.3:c.1724A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001144735Athena Diagnostics Inccriteria provided, single submitter
Pathogenic
(Aug 6, 2019)
germlineclinical testing

PubMed (15)
[See all records that cite these PMIDs]

SCV002013467GeneDxcriteria provided, single submitter
Pathogenic
(Oct 7, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

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

Citations

PubMed

The use of next-generation sequencing in molecular diagnosis of neurofibromatosis type 1: a validation study.

Maruoka R, Takenouchi T, Torii C, Shimizu A, Misu K, Higasa K, Matsuda F, Ota A, Tanito K, Kuramochi A, Arima Y, Otsuka F, Yoshida Y, Moriyama K, Niimura M, Saya H, Kosaki K.

Genet Test Mol Biomarkers. 2014 Nov;18(11):722-35. doi: 10.1089/gtmb.2014.0109. Epub 2014 Oct 17.

PubMed [citation]
PMID:
25325900
PMCID:
PMC4216997

Molecular diagnosis of neurofibromatosis type 1: 2 years experience.

Griffiths S, Thompson P, Frayling I, Upadhyaya M.

Fam Cancer. 2007;6(1):21-34.

PubMed [citation]
PMID:
16944272
See all PubMed Citations (15)

Details of each submission

From Athena Diagnostics Inc, SCV001144735.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (15)

Description

Not found in the total gnomAD dataset, and the data is high quality (0/263140 chr). Variant has been found in 6 or more unrelated symptomatic patients, while absent in large general pop studies. Predicted to negatively affect a known splice site. Damaging to protein function(s) relevant to disease mechanism. Inconclusive segregation with disease.

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

From GeneDx, SCV002013467.1

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

Description

Non-canonical splice site variant demonstrated to result in skipping of exon 11 (Violante 2013, Esposito 2015); In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing; Not observed in large population cohorts (Lek 2016); Also known as IVS15+3A>G; This variant is associated with the following publications: (PMID: 19845691, 26478990, 7981679, 23404336, 18546366, 26056819, 15146469, 28008555, 10607834, 16944272, 26969325, 10712197, 16380919, 32352596, 31713330, 31370276, 31776437)

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

Last Updated: Nov 27, 2021

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