NM_004333.6(BRAF):c.2128-27_2128-18del AND not specified

Germline classification:: Benign (1 submission)
Last evaluated:: Oct 21, 2019
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:: RCV001193861.1

Allele description [Variation Report for NM_004333.6(BRAF):c.2128-27_2128-18del]

NM_004333.6(BRAF):c.2128-27_2128-18del

Gene:

BRAF:B-Raf proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

7q34

Genomic location:

Preferred name:

NM_004333.6(BRAF):c.2128-27_2128-18del

HGVS:

NC_000007.14:g.140734788_140734797del
NC_000007.14:g.140734794AAAGAAAAAA[1]
NG_007873.3:g.194958CTTTTTTTTT[1]
NM_001354609.2:c.2128-27_2128-18del
NM_001374244.1:c.2248-27_2248-18del
NM_001374258.1:c.2248-27_2248-18del
NM_001378467.1:c.2137-27_2137-18del
NM_001378468.1:c.2127+5015_2127+5024del
NM_001378469.1:c.2062-27_2062-18del
NM_001378470.1:c.2026-27_2026-18del
NM_001378471.1:c.2017-27_2017-18del
NM_001378472.1:c.1972-27_1972-18del
NM_001378473.1:c.1972-27_1972-18del
NM_001378474.1:c.2127+5015_2127+5024del
NM_001378475.1:c.1864-27_1864-18del
NM_004333.6:c.2128-27_2128-18delMANE SELECT
LRG_299t1:c.2128-27_2128-18del
LRG_299:g.194958CTTTTTTTTT[1]
NC_000007.13:g.140434588_140434597del
NC_000007.13:g.140434594AAAGAAAAAA[1]
NM_004333.4:c.2128-27_2128-18del

Links:

dbSNP: rs774138098

NCBI 1000 Genomes Browser:

rs774138098

Molecular consequence:

NM_001354609.2:c.2128-27_2128-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001374244.1:c.2248-27_2248-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001374258.1:c.2248-27_2248-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378467.1:c.2137-27_2137-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378468.1:c.2127+5015_2127+5024del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378469.1:c.2062-27_2062-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378470.1:c.2026-27_2026-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378471.1:c.2017-27_2017-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378472.1:c.1972-27_1972-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378473.1:c.1972-27_1972-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378474.1:c.2127+5015_2127+5024del - intron variant - [Sequence Ontology: SO:0001627]
NM_001378475.1:c.1864-27_1864-18del - intron variant - [Sequence Ontology: SO:0001627]
NM_004333.6:c.2128-27_2128-18del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001363011	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Oct 21, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001363011

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Oct 21, 2019)

germline

clinical testing

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

Citation Link

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

Acquired initiating mutations in early hematopoietic cells of CLL patients.

Damm F, Mylonas E, Cosson A, Yoshida K, Della Valle V, Mouly E, Diop M, Scourzic L, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Kikushige Y, Davi F, Lambert J, Gautheret D, Merle-Béral H, Sutton L, Dessen P, Solary E, Akashi K, Vainchenker W, et al.

Cancer Discov. 2014 Sep;4(9):1088-101. doi: 10.1158/2159-8290.CD-14-0104. Epub 2014 Jun 11.

PubMed [citation]

PMID:: 24920063

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001363011.1

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

Description

Variant summary: BRAF c.2128-27_2128-18del10 deletes ten nucleotides located close to a canonical splice site and therefore could affect mRNA splicing. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.01 in 143638 control chromosomes, predominantly at a frequency of 0.035 within the African or African-American subpopulation in the gnomAD database, including 33 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 14000 fold of the estimated maximal expected allele frequency for a pathogenic variant in BRAF causing Noonan Syndrome and Related Conditions phenotype (2.5e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.2128-27_2128-18del10 in individuals affected with Noonan Syndrome and Related Conditions and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.

#	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: Mar 22, 2025

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