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NM_001354689.3(RAF1):c.124_125delinsAT (p.Ala42Ile)

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Interpretation:
Likely benign​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
7 (Most recent: Sep 15, 2021)
Last evaluated:
Sep 24, 2019
Accession:
VCV000229175.10
Variation ID:
229175
Description:
2bp indel
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NM_001354689.3(RAF1):c.124_125delinsAT (p.Ala42Ile)

Allele ID
229019
Variant type
Indel
Variant length
2 bp
Cytogenetic location
3p25.2
Genomic location
3: 12618597-12618598 (GRCh38) GRCh38 UCSC
3: 12660096-12660097 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_002880.3:c.124_125delGCinsAT missense
LRG_413:g.50582_50583delinsAT
LRG_413t2:c.124_125delinsAT LRG_413p2:p.Ala42Ile
... more HGVS
Protein change
A42I
Other names
-
Canonical SPDI
NC_000003.12:12618596:GC:AT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10576608
dbSNP: rs876657965
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 reviewed by expert panel Sep 24, 2019 RCV000461796.7
Uncertain significance 1 criteria provided, single submitter - RCV000845521.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 5, 2019 RCV000219930.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 26, 2017 RCV000589194.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
RAF1 No evidence available No evidence available GRCh38
GRCh37
559 612

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Sep 24, 2019)
reviewed by expert panel
Method: curation
Rasopathy
(Autosomal dominant inheritance)
Allele origin: germline
ClinGen RASopathy Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV001192867.1
Submitted: (Mar 06, 2020)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.124_125delinsAT (p.Ala42Ile) variant in RAF1 is reported in population databases as two contiguous missense variants: c.124G>A and c.125C>T in cis in 27/64,595 (0.03%) European … (more)
Uncertain significance
(Nov 26, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000858114.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Sep 05, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000698121.2
Submitted: (Sep 24, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: RAF1 c.124_125delinsAT (p.Ala42Ile) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging … (more)
Uncertain significance
(Nov 03, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000272341.3
Submitted: (Mar 21, 2019)
Evidence details
Comment:
The p.Ala42Ile variant in RAF1 has not been previously reported in individuals w ith a RASopathy, but has been identified by our laboratory in 1 … (more)
Uncertain significance
(-)
criteria provided, single submitter
Method: clinical testing
Primary familial hypertrophic cardiomyopathy
Allele origin: germline
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease,Montreal Heart Institute
Accession: SCV000987624.1
Submitted: (Feb 19, 2019)
Evidence details
Uncertain significance
(Oct 13, 2020)
criteria provided, single submitter
Method: clinical testing
Rasopathy
Allele origin: germline
Invitae
Accession: SCV000552093.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This variant, c.124_125delGCinsAT, is a complex sequence change that results in a missense change substituting alanine for isoleucine at codon 42 of the RAF1 protein … (more)
Benign
(Sep 16, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001871429.1
Submitted: (Sep 15, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Molecular analysis of sarcomeric and non-sarcomeric genes in patients with hypertrophic cardiomyopathy. Bottillo I Gene 2016 PMID: 26656175
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=RAF1 - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/919f50ca-3d8b-43ff-8ea0-a44b985bc2e3 - - - -

Text-mined citations for rs876657965...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 23, 2021