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

Clinical significance:Benign (Last evaluated: Apr 18, 2017)

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000459831.6

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

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

Gene:
RAF1:Raf-1 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.2
Genomic location:
Preferred name:
NM_001354689.3(RAF1):c.1689G>C (p.Thr563=)
Other names:
p.T543T; NM_002880.3(RAF1):c.1629G>C
HGVS:
  • 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
Links:
dbSNP: rs5746244
NCBI 1000 Genomes Browser:
rs5746244
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]

Condition(s)

Name:
Rasopathy
Synonyms:
rasopathies; Noonan spectrum disorder
Identifiers:
MONDO: MONDO:0021060; MedGen: CN166718

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000562253Invitaecriteria provided, single submitter
Likely benign
(Nov 4, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000616483ClinGen RASopathy Variant Curation Expert Panelreviewed by expert panel
Benign
(Apr 18, 2017)
germlinecuration

Citation Link

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000562253.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From ClinGen RASopathy Variant Curation Expert Panel, SCV000616483.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

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, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BA1; PMID:29493581)

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

Last Updated: Aug 27, 2021

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