NC_000017.10:g.(?_29496899)_(29701173_?)del AND Neurofibromatosis, type 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 16, 2021
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:: RCV001949414.8

Allele description [Variation Report for NC_000017.10:g.(?_29496899)_(29701173_?)del]

NC_000017.10:g.(?_29496899)_(29701173_?)del

Genes:: EVI2A:ecotropic viral integration site 2A [Gene - OMIM - HGNC]
EVI2B:ecotropic viral integration site 2B [Gene - OMIM - HGNC]
OMG:oligodendrocyte myelin glycoprotein [Gene - OMIM - HGNC]
NF1:neurofibromin 1 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 17q11.2
Genomic location:: Chr17: 29496899 - 29701173 (on Assembly GRCh37)
Preferred name:: NC_000017.10:g.(?_29496899)_(29701173_?)del
HGVS:: NC_000017.10:g.(?_29496899)_(29701173_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Neurofibromatosis, type 1 (NF1)
Synonyms:: NEUROFIBROMATOSIS, TYPE I; Recklinghausen's disease; Von Recklinghausen disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018975; MedGen: C0027831; Orphanet: 636; OMIM: 162200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002239051	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 16, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002239051

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 16, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002239051.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

For these reasons, this variant has been classified as Pathogenic. Sub-genic deletion of exons 9-12, 40-45, 36-56 and 32-57 have been determined to be pathogenic (PMID:¬†26189818, 18196300,¬†Invitae). Therefore, deletions that fully encompass that region are also expected to be pathogenic. A similar deletion of exons 5-57 has been reported in an individual affected with neurofibromatosis type I (PMID:¬†26189818). This variant is a gross deletion of the genomic region encompassing exons 5-57 of the NF1 gene. The 5' boundary is likely confined to intron 5. The 3' end of this event is unknown as it extends through the termination codon beyond the assayed region for this gene and may encompass additional genes. While this deletion is not anticipated to result in nonsense mediated decay, it is expected to create a truncated protein product or disrupt mRNA translation.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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