NM_001042492.3(NF1):c.7153AACTTT[1] (p.2385NF[1]) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Jun 17, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000680827.33

Allele description [Variation Report for NM_001042492.3(NF1):c.7153AACTTT[1] (p.2385NF[1])]

NM_001042492.3(NF1):c.7153AACTTT[1] (p.2385NF[1])

Gene:

NF1:neurofibromin 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

17q11.2

Genomic location:

Preferred name:

NM_001042492.3(NF1):c.7153AACTTT[1] (p.2385NF[1])

HGVS:

NC_000017.11:g.31343099AACTTT[1]
NG_009018.1:g.253123AACTTT[1]
NM_000267.3:c.7090AACTTT[1]
NM_000267.3:c.7096_7101del
NM_001042492.3:c.7153AACTTT[1]MANE SELECT
NP_000258.1:p.2364NF[1]
NP_001035957.1:p.2385NF[1]
LRG_214t1:c.7090AACTTT[1]
LRG_214:g.253123AACTTT[1]
LRG_214p1:p.2364NF[1]
NC_000017.10:g.29670116_29670121del
NC_000017.10:g.29670117AACTTT[1]
NM_000267.3:c.7096_7101del
NM_000267.3:c.7096_7101delAACTTT
NM_001042492.2:c.7159_7164del
NM_001042492.2:c.7159_7164del6
NM_001042492.3:c.7153AACTTT[1]

Links:

dbSNP: rs864622639

NCBI 1000 Genomes Browser:

rs864622639

Molecular consequence:

NM_000267.3:c.7090AACTTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001042492.3:c.7153AACTTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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SRX6623291 (1)
SRA
Glochidion cf. rubrum SO-2022 1311311 chloroplast matK gene for maturase K, part...
Glochidion cf. rubrum SO-2022 1311311 chloroplast matK gene for maturase K, partial cds
gi|2349427976|dbj|LC737107.1|

Nucleotide
molybdenum cofactor biosynthesis protein MoeA [Acinetobacter baumannii]
molybdenum cofactor biosynthesis protein MoeA [Acinetobacter baumannii]
gi|803657330|gb|AIA51080.2||gnl|PRJ 628|BL01_04485

Protein
22-benzoyloxy-3,16,28-trihydroxyolean-12-ene 3-O-(glucopyranosyl-1-3-arabinopyra...
22-benzoyloxy-3,16,28-trihydroxyolean-12-ene 3-O-(glucopyranosyl-1-3-arabinopyranoside) [Supplementary Concept]
has antineoplastic activity; isolated from Glochidion eriocarpum; structure in first source<br/>Date introduced: April 2, 2009<br/>

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000808275	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (May 11, 2022)	germline	clinical testing	Citation Link,
SCV001249056	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Dec 1, 2019)	germline	clinical testing	Citation Link,
SCV002503006	AiLife Diagnostics, AiLife Diagnostics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 28, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 8081387, 31533797, 25741868
SCV002771573	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Jun 17, 2022)	unknown	clinical testing	PubMed (18) [See all records that cite these PMIDs] 33372952, 31533797, 34427956, 32405727, 31766501, 32024963, 12807981, 22962301, 18546366, 8081387, 10862084, 24789688, 25541118, 25293717, 28924536, 27838393, 30014477, 26467025

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	4	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Germline Cancer Predisposition Variants in Pediatric Rhabdomyosarcoma: A Report From the Children's Oncology Group.

Li H, Sisoudiya SD, Martin-Giacalone BA, Khayat MM, Dugan-Perez S, Marquez-Do DA, Scheurer ME, Muzny D, Boerwinkle E, Gibbs RA, Chi YY, Barkauskas DA, Lo T, Hall D, Stewart DR, Schiffman JD, Skapek SX, Hawkins DS, Plon SE, Sabo A, Lupo PJ.

J Natl Cancer Inst. 2021 Jul 1;113(7):875-883. doi: 10.1093/jnci/djaa204.

PubMed [citation]

PMID:: 33372952
PMCID:: PMC8246828

See all PubMed Citations (19)

Details of each submission

From GeneDx, SCV000808275.3

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

Description

In-frame deletion of 2 amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as p.2366delNF; This variant is associated with the following publications: (PMID: 32405727, 25293717, 18546366, 12807981, 25541118, 10862084, 8081387, 30014477, 31766501, 31533797, 31776437, 33372952)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001249056.26

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		3	not provided	not provided	not provided

From AiLife Diagnostics, AiLife Diagnostics, SCV002503006.1

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

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

From Athena Diagnostics, SCV002771573.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (18)

Description

This variant has been identified in multiple unrelated individuals with clinical features of NF1, including at least one apparent de novo case. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In some published literature, this variant is referred to as c.7159_7164del.

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

Last Updated: Oct 26, 2024

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