NM_004333.6(BRAF):c.2128-16delinsTCT AND not specified

Germline classification:: Benign (1 submission)
Last evaluated:: Dec 22, 2020
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:: RCV001280678.1

Allele description [Variation Report for NM_004333.6(BRAF):c.2128-16delinsTCT]

NM_004333.6(BRAF):c.2128-16delinsTCT

Gene:

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

Variant type:

Indel

Cytogenetic location:

7q34

Genomic location:

Preferred name:

NM_004333.6(BRAF):c.2128-16delinsTCT

HGVS:

NC_000007.14:g.140734786delinsAGA
NG_007873.3:g.194979delinsTCT
NM_001354609.2:c.2128-16delinsTCT
NM_001374244.1:c.2248-16delinsTCT
NM_001374258.1:c.2248-16delinsTCT
NM_001378467.1:c.2137-16delinsTCT
NM_001378468.1:c.2127+5026delinsTCT
NM_001378469.1:c.2062-16delinsTCT
NM_001378470.1:c.2026-16delinsTCT
NM_001378471.1:c.2017-16delinsTCT
NM_001378472.1:c.1972-16delinsTCT
NM_001378473.1:c.1972-16delinsTCT
NM_001378474.1:c.2127+5026delinsTCT
NM_001378475.1:c.1864-16delinsTCT
NM_004333.6:c.2128-16delinsTCTMANE SELECT
LRG_299t1:c.2128-16delinsTCT
LRG_299:g.194979delinsTCT
NC_000007.13:g.140434586delinsAGA
NM_004333.4:c.2128-16delinsTCT

Links:

dbSNP: rs1796250484

NCBI 1000 Genomes Browser:

rs1796250484

Molecular consequence:

NM_001354609.2:c.2128-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001374244.1:c.2248-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001374258.1:c.2248-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378467.1:c.2137-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378468.1:c.2127+5026delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378469.1:c.2062-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378470.1:c.2026-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378471.1:c.2017-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378472.1:c.1972-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378473.1:c.1972-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378474.1:c.2127+5026delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_001378475.1:c.1864-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]
NM_004333.6:c.2128-16delinsTCT - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Nucleotide
Tapinoma melanocephalum
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001467976	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Dec 22, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001467976

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Dec 22, 2020)

germline

clinical testing

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001467976.1

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

Description

Variant summary: BRAF c.2128-16delinsTCT alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 159536 control chromosomes (gnomAD), however the variant is located to a highly polymorphic poly-T region, where several similar variants occur with a high allele frequency, suggesting that this variant could be a benign polymorphism. To our knowledge, no occurrence of c.2128-16delinsTCT in individuals affected with Cardiofaciocutaneous Syndrome 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: Sep 17, 2022

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