NM_002880.4(RAF1):c.856G>A (p.Glu286Lys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 13, 2016
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:: RCV000586626.1

Allele description [Variation Report for NM_002880.4(RAF1):c.856G>A (p.Glu286Lys)]

NM_002880.4(RAF1):c.856G>A (p.Glu286Lys)

Gene:

RAF1:Raf-1 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.2

Genomic location:

Preferred name:

NM_002880.4(RAF1):c.856G>A (p.Glu286Lys)

HGVS:

NC_000003.12:g.12600394C>T
NG_007467.1:g.68786G>A
NM_001354689.3:c.916G>A
NM_001354690.3:c.856G>A
NM_001354691.3:c.613G>A
NM_001354692.3:c.613G>A
NM_001354693.3:c.757G>A
NM_001354694.3:c.673G>A
NM_001354695.3:c.514G>A
NM_002880.4:c.856G>AMANE SELECT
NP_001341618.1:p.Glu306Lys
NP_001341619.1:p.Glu286Lys
NP_001341620.1:p.Glu205Lys
NP_001341621.1:p.Glu205Lys
NP_001341622.1:p.Glu253Lys
NP_001341623.1:p.Glu225Lys
NP_001341624.1:p.Glu172Lys
NP_002871.1:p.Glu286Lys
NP_002871.1:p.Glu286Lys
LRG_413t1:c.856G>A
LRG_413t2:c.916G>A
LRG_413:g.68786G>A
LRG_413p1:p.Glu286Lys
LRG_413p2:p.Glu306Lys
NC_000003.11:g.12641893C>T
NM_002880.3:c.856G>A
NR_148940.3:n.1187G>A
NR_148941.3:n.1187G>A
NR_148942.3:n.1187G>A

Protein change:

E172K

Links:

dbSNP: rs147453956

NCBI 1000 Genomes Browser:

rs147453956

Molecular consequence:

NM_001354689.3:c.916G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354690.3:c.856G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354691.3:c.613G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354692.3:c.613G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354693.3:c.757G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354694.3:c.673G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354695.3:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002880.4:c.856G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148940.3:n.1187G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148941.3:n.1187G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148942.3:n.1187G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000698131	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Mar 13, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000698131

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Mar 13, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx

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, SCV000698131.1

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

Description

Variant summary: c.856G>A in RAF1 gene affects a highly conserved nucleotide, resulting in amino acid change from Glu to Lys. 3/4 in-silico tools predict this variant to be benign. The variant is found in the large control population datasets of ExAC and 1000Gs at an overall frequency of 0.00176% exclusively in individuals of East Asian origin. This frequency does not exceed the maximum expected allele frequency for a pathogenic RAF1 variant (0.0025%). The variant of interest has not, to our knowledge, been reported in affected individuals via publications or disease-specific databases/diagnostic centers. Taken together, the variant was classified as a variant of uncertain significance (VUS) until additional information becomes available.

#	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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