NM_001354689.3(RAF1):c.1689G>C (p.Thr563=) AND Noonan syndrome 5

Clinical significance:Likely benign (Last evaluated: Apr 27, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001354689.3(RAF1):c.1689G>C (p.Thr563=)]

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

RAF1:Raf-1 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001354689.3(RAF1):c.1689G>C (p.Thr563=)
Other names:
p.T543T; NM_002880.3(RAF1):c.1629G>C
  • NC_000003.12:g.12585161C>G
  • NG_007467.1:g.84019G>C
  • NM_001354689.3:c.1689G>CMANE SELECT
  • NM_001354690.2:c.1629G>C
  • NM_001354691.2:c.1386G>C
  • NM_001354692.2:c.1386G>C
  • NM_001354693.2:c.1530G>C
  • NM_001354694.2:c.1446G>C
  • NM_001354695.2:c.1287G>C
  • NM_002880.3:c.1629G>C
  • NP_001341618.1:p.Thr563=
  • NP_001341619.1:p.Thr543=
  • NP_001341620.1:p.Thr462=
  • NP_001341621.1:p.Thr462=
  • NP_001341622.1:p.Thr510=
  • NP_001341623.1:p.Thr482=
  • NP_001341624.1:p.Thr429=
  • NP_002871.1:p.Thr543=
  • LRG_413t1:c.1629G>C
  • LRG_413t2:c.1689G>C
  • LRG_413:g.84019G>C
  • LRG_413p1:p.Thr543=
  • LRG_413p2:p.Thr563=
  • NC_000003.11:g.12626660C>G
  • NR_148940.2:n.2073G>C
  • NR_148941.2:n.2019G>C
  • NR_148942.2:n.1958G>C
  • p.Thr543Thr
dbSNP: rs5746244
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NR_148940.2:n.2073G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148941.2:n.2019G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148942.2:n.1958G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001354689.3:c.1689G>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354690.2:c.1629G>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354691.2:c.1386G>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354692.2:c.1386G>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354693.2:c.1530G>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354694.2:c.1446G>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001354695.2:c.1287G>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_002880.3:c.1629G>C - synonymous variant - [Sequence Ontology: SO:0001819]


Noonan syndrome 5 (NS5)
RAF1 gene related Noonan syndrome
MONDO: MONDO:0012690; MedGen: C1969057; Orphanet: 648; OMIM: 611553

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001309553Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV001309553.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


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, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 27, 2021

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