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NM_001042492.3(NF1):c.1062+3A>G AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 19, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000437730.2

Allele description [Variation Report for NM_001042492.3(NF1):c.1062+3A>G]

NM_001042492.3(NF1):c.1062+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.1062+3A>G
HGVS:
  • NC_000017.11:g.31200598A>G
  • NG_009018.1:g.110622A>G
  • NM_000267.3:c.1062+3A>G
  • NM_001042492.3:c.1062+3A>GMANE SELECT
  • NM_001128147.3:c.1062+3A>G
  • LRG_214t1:c.1062+3A>G
  • LRG_214:g.110622A>G
  • NC_000017.10:g.29527616A>G
  • NM_001042492.3:c.1062+3A>G
Links:
dbSNP: rs1057521098
NCBI 1000 Genomes Browser:
rs1057521098
Molecular consequence:
  • NM_000267.3:c.1062+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001042492.3:c.1062+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001128147.3:c.1062+3A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000521059GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Dec 19, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000521059.4

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

Description

The c.1062+3 A>G variant has been published previously in association with neurofibromatosis type 1 (Pros et al., 2008). The variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Several in-silico splice prediction models predict that c.1062+3 A>G destroys the natural splice donor site of intron 9. Additionally, mRNA studies have suggested that the variant results in skipping of exon 9 (Pros et al., 2008); however, these studies were performed using patient mRNA, and in vitro functional studies have yet to be performed. Therefore, we consider this variant to be likely pathogenic.

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

Last Updated: Sep 29, 2024