NM_002880.4(RAF1):c.1777_1782del (p.Lys593_Glu594del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 8, 2023
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:: RCV003442295.1

Allele description [Variation Report for NM_002880.4(RAF1):c.1777_1782del (p.Lys593_Glu594del)]

NM_002880.4(RAF1):c.1777_1782del (p.Lys593_Glu594del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p25.2

Genomic location:

Preferred name:

NM_002880.4(RAF1):c.1777_1782del (p.Lys593_Glu594del)

HGVS:

NC_000003.12:g.12584869_12584874del
NG_007467.1:g.84307_84312del
NM_001354689.3:c.1837_1842del
NM_001354690.3:c.1777_1782del
NM_001354691.3:c.1534_1539del
NM_001354692.3:c.1534_1539del
NM_001354693.3:c.1678_1683del
NM_001354694.3:c.1594_1599del
NM_001354695.3:c.1435_1440del
NM_002880.4:c.1777_1782delMANE SELECT
NP_001341618.1:p.Lys613_Glu614del
NP_001341619.1:p.Lys593_Glu594del
NP_001341620.1:p.Lys512_Glu513del
NP_001341621.1:p.Lys512_Glu513del
NP_001341622.1:p.Lys560_Glu561del
NP_001341623.1:p.Lys532_Glu533del
NP_001341624.1:p.Lys479_Glu480del
NP_002871.1:p.Lys593_Glu594del
NP_002871.1:p.Lys593_Glu594del
LRG_413t1:c.1777_1782del
LRG_413t2:c.1837_1842del
LRG_413:g.84307_84312del
LRG_413p2:p.Lys613_Glu614del
NC_000003.11:g.12626368_12626373del
NM_002880.3:c.1776_1781delAAAGGA
NM_002880.3:c.1777_1782del
NR_148940.3:n.2221_2226del
NR_148941.3:n.2167_2172del
NR_148942.3:n.2106_2111del

Molecular consequence:

NM_001354689.3:c.1837_1842del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354690.3:c.1777_1782del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354691.3:c.1534_1539del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354692.3:c.1534_1539del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354693.3:c.1678_1683del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354694.3:c.1594_1599del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354695.3:c.1435_1440del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_002880.4:c.1777_1782del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_148940.3:n.2221_2226del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148941.3:n.2167_2172del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148942.3:n.2106_2111del - 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
SCV004169782	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 8, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004169782

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 8, 2023)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV004169782.1

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of 2 amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 29493581)

#	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

Last Updated: Nov 25, 2023

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