NM_000268.4(NF2):c.886-3C>T AND Neurofibromatosis, type 2

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Oct 27, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV001062375.8

Allele description [Variation Report for NM_000268.4(NF2):c.886-3C>T]

NM_000268.4(NF2):c.886-3C>T

Gene:

NF2:NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.2

Genomic location:

Preferred name:

NM_000268.4(NF2):c.886-3C>T

HGVS:

NC_000022.11:g.29668330C>T
NG_009057.1:g.69775C>T
NM_000268.4:c.886-3C>TMANE SELECT
NM_016418.5:c.886-3C>T
NM_181825.3:c.886-3C>T
NM_181828.3:c.760-3C>T
NM_181829.3:c.763-3C>T
NM_181830.3:c.637-3C>T
NM_181831.3:c.637-3C>T
NM_181832.3:c.886-3C>T
NM_181833.3:c.447+26045C>T
LRG_511t1:c.886-3C>T
LRG_511t2:c.886-3C>T
LRG_511:g.69775C>T
NC_000022.10:g.30064319C>T
NM_000268.3:c.886-3C>T

Links:

dbSNP: rs1340263866

NCBI 1000 Genomes Browser:

rs1340263866

Molecular consequence:

NM_000268.4:c.886-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_016418.5:c.886-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_181825.3:c.886-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_181828.3:c.760-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_181829.3:c.763-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_181830.3:c.637-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_181831.3:c.637-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_181832.3:c.886-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_181833.3:c.447+26045C>T - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Name:: Neurofibromatosis, type 2 (SWNV)
Synonyms:: NF 2; Neurofibromatosis central type; Acoustic schwannomas bilateral; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007039; MedGen: C0027832; Orphanet: 637; OMIM: 101000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001227171	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 13, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532
SCV004843693	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Oct 27, 2023)	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

SCV001227171

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 13, 2019)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004843693

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely Benign
(Oct 27, 2023)

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	1	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001227171.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 9 of the NF2 gene. It does not directly change the encoded amino acid sequence of the NF2 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant has not been reported in the literature in individuals with NF2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing, but this prediction has not been confirmed by published transcriptional studies.

#	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

From All of Us Research Program, National Institutes of Health, SCV004843693.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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