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NM_001354689.3(RAF1):c.1974G>A (p.Thr658=)

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Interpretation:
Benign​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
9 (Most recent: Sep 22, 2021)
Last evaluated:
Apr 18, 2017
Accession:
VCV000040628.10
Variation ID:
40628
Description:
single nucleotide variant
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NM_001354689.3(RAF1):c.1974G>A (p.Thr658=)

Allele ID
49098
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.2
Genomic location
3: 12584547 (GRCh38) GRCh38 UCSC
3: 12626046 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.12626046C>T
NC_000003.12:g.12584547C>T
NG_007467.1:g.84633G>A
... more HGVS
Protein change
-
Other names
p.T638T
NM_002880.3(RAF1):c.1914G>A
Canonical SPDI
NC_000003.12:12584546:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00359 (T)

Allele frequency
1000 Genomes Project 0.00359
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Links
ClinGen: CA134715
dbSNP: rs144876026
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 reviewed by expert panel Apr 18, 2017 RCV000519653.6
Benign 3 criteria provided, multiple submitters, no conflicts Aug 30, 2019 RCV000037684.6
Benign 1 criteria provided, single submitter May 21, 2015 RCV000242024.2
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000279428.3
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000402345.3
Benign 1 criteria provided, single submitter Mar 3, 2015 RCV001705628.1
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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
(Apr 18, 2017)
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: SCV000616478.3
Submitted: (Feb 25, 2019)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The filtering allele frequency of the c.1914G>A (p.Thr638=) variant in the RAF1 gene is 0.926% (174/16512) of South Asian chromosomes by the Exome Aggregation Consortium, … (more)
Benign
(Aug 30, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001360610.1
Submitted: (Mar 06, 2020)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000309260.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
LEOPARD syndrome 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000440615.3
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
(May 21, 2015)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000319656.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(Aug 10, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000061346.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Thr638Thr in exon 17 of RAF1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue … (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: SCV000440616.3
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
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Rasopathy
Allele origin: germline
Invitae
Accession: SCV000659055.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001915674.1
Submitted: (Sep 22, 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/5dd1c397-b2a2-4954-bbbb-583d4a4576dc - - - -

Text-mined citations for rs144876026...

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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 26, 2021