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NM_001354689.3(RAF1):c.94A>G (p.Ile32Val)

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Interpretation:
Benign​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 27, 2019
Accession:
VCV000040584.8
Variation ID:
40584
Description:
single nucleotide variant
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NM_001354689.3(RAF1):c.94A>G (p.Ile32Val)

Allele ID
49054
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.2
Genomic location
3: 12618628 (GRCh38) GRCh38 UCSC
3: 12660127 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.12660127T>C
NC_000003.12:g.12618628T>C
NG_007467.1:g.50552A>G
... more HGVS
Protein change
I32V
Other names
p.I32V:ATA>GTA
NM_002880.3(RAF1):c.94A>G
Canonical SPDI
NC_000003.12:12618627:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00011
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Trans-Omics for Precision Medicine (TOPMed) 0.00021
The Genome Aggregation Database (gnomAD), exomes 0.00010
The Genome Aggregation Database (gnomAD) 0.00025
Links
ClinGen: CA241481
dbSNP: rs372738063
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 reviewed by expert panel Jun 27, 2019 RCV000788000.1
Likely benign 3 criteria provided, multiple submitters, no conflicts Aug 22, 2021 RCV000159060.8
Uncertain significance 1 criteria provided, single submitter Oct 28, 2020 RCV000229182.7
Likely benign 1 criteria provided, single submitter Aug 9, 2018 RCV000680302.1
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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
556 609

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jun 27, 2019)
reviewed by expert panel
Method: curation
Noonan syndrome and Noonan-related syndrome
(Autosomal dominant inheritance)
Allele origin: germline
ClinGen RASopathy Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV000927032.1
Submitted: (Jul 15, 2019)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.94A>G (p.Ile32Val) variant in the RAF1 gene has been identified in patients who underwent testing for a RASopathy, however it has also been identified … (more)
Likely benign
(Aug 09, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000209002.14
Submitted: (Sep 14, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Aug 21, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000227277.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Oct 28, 2020)
criteria provided, single submitter
Method: clinical testing
Rasopathy
Allele origin: germline
Invitae
Accession: SCV000287747.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces isoleucine with valine at codon 32 of the RAF1 protein (p.Ile32Val). The isoleucine residue is highly conserved and there is a … (more)
Likely benign
(Aug 22, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001339226.2
Submitted: (Apr 29, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: RAF1 c.94A>G (p.Ile32Val) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign … (more)
Likely benign
(Mar 19, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000966503.1
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Ile32Val in exon2 of RAF1: This variant has been identified in 0.02% (22/12673 0) of European chromosomes and 0.03% (6/24036) of African chromosomes by the … (more)

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
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811
Germline Mutations in Predisposition Genes in Pediatric Cancer. Zhang J The New England journal of medicine 2015 PMID: 26580448
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=RAF1 - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/1128f941-c33c-438d-a44d-f5a0c76c3440 - - - -

Text-mined citations for rs372738063...

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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 07, 2021