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NM_001354689.3(RAF1):c.1689G>C (p.Thr563=)

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Interpretation:
Benign​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
7 (Most recent: Jul 16, 2021)
Last evaluated:
Apr 18, 2017
Accession:
VCV000040621.6
Variation ID:
40621
Description:
single nucleotide variant
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NM_001354689.3(RAF1):c.1689G>C (p.Thr563=)

Allele ID
49091
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.2
Genomic location
3: 12585161 (GRCh38) GRCh38 UCSC
3: 12626660 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001354691.2:c.1386G>C NP_001341620.1:p.Thr462= synonymous
NM_001354692.2:c.1386G>C NP_001341621.1:p.Thr462= synonymous
NM_001354693.2:c.1530G>C NP_001341622.1:p.Thr510= synonymous
... more HGVS
Protein change
-
Other names
p.T543T
NM_002880.3(RAF1):c.1629G>C
Canonical SPDI
NC_000003.12:12585160:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00007
1000 Genomes Project 0.00100
Links
ClinGen: CA235376
dbSNP: rs5746244
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 RCV000459831.6
Benign 3 criteria provided, multiple submitters, no conflicts Jun 27, 2016 RCV000157703.5
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV001146462.1
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV001148647.1
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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
(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: SCV000616483.3
Submitted: (Feb 25, 2019)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The filtering allele frequency of the c.1629G>C (p.Thr543=) variant in the RAF1 gene is 0.054% (9/8654) of East Asian chromosomes by the Exome Aggregation Consortium, … (more)
Likely benign
(Nov 04, 2020)
criteria provided, single submitter
Method: clinical testing
Rasopathy
Allele origin: germline
Invitae
Accession: SCV000562253.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jun 27, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000698122.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: The RAF1 c.1629G>C (p.Thr543Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a … (more)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
LEOPARD syndrome 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001307208.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Noonan syndrome 5
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001309553.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001752916.1
Submitted: (Jul 16, 2021)
Evidence details
Uncertain significance
(Jan 15, 2015)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Greenwood Genetic Center Diagnostic Laboratories,Greenwood Genetic Center
Accession: SCV000207691.1
Submitted: (Jan 20, 2015)
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
No mutation in RAS-MAPK pathway genes in 30 patients with Kabuki syndrome. Kuniba H American journal of medical genetics. Part A 2008 PMID: 18553519
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/72d45c95-18bf-47fe-a2fa-b6ca719e877f - - - -

Text-mined citations for rs5746244...

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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 Aug 27, 2021