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NM_001354689.3(RAF1):c.-267G>A

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Interpretation:
Benign​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
5 (Most recent: Sep 28, 2021)
Last evaluated:
Jul 25, 2019
Accession:
VCV000040575.5
Variation ID:
40575
Description:
single nucleotide variant
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NM_001354689.3(RAF1):c.-267G>A

Allele ID
49045
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.2
Genomic location
3: 12664053 (GRCh38) GRCh38 UCSC
3: 12705552 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_002880.3(RAF1):c.-267G>A 5 prime UTR
NC_000003.11:g.12705552C>T
NG_007467.1:g.5127G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:12664052:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00220 (T)

Allele frequency
1000 Genomes Project 0.00220
Trans-Omics for Precision Medicine (TOPMed) 0.00201
Links
ClinGen: CA181005
dbSNP: rs116247741
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 Jul 25, 2019 RCV001030073.1
Likely benign 1 criteria provided, single submitter Nov 17, 2011 RCV000154580.1
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000291471.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000344111.2
Benign 1 criteria provided, single submitter Mar 3, 2015 RCV001711142.1
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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
566 619

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 25, 2019)
reviewed by expert panel
Method: curation
Rasopathy
(Autosomal dominant inheritance)
Allele origin: germline
ClinGen RASopathy Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV001192861.1
Submitted: (Mar 06, 2020)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.-267G>A variant was identified in the RAF1 gene. The filtering allele frequency for the c.-267G>A is 6.32% for African chromosomes in gnomAD (68/8706 with … (more)
Likely benign
(Nov 17, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000204253.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
This variant is located in the 5'UTR and variants in regulatory regions could ha ve an effect on transcriptional or translational efficiency. However, variants o … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
LEOPARD syndrome 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000440654.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Noonan syndrome 5
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000440653.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001945716.1
Submitted: (Sep 28, 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
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/8ca8203f-7106-4509-94f8-6bfbd5481879 - - - -

Text-mined citations for rs116247741...

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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 Oct 02, 2021