NM_000540.3(RYR1):c.7089C>T (p.Cys2363=) AND not specified

Germline classification:: Benign (5 submissions)
Last evaluated:: Mar 29, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000079161.22

Allele description [Variation Report for NM_000540.3(RYR1):c.7089C>T (p.Cys2363=)]

NM_000540.3(RYR1):c.7089C>T (p.Cys2363=)

Gene:

RYR1:ryanodine receptor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.2

Genomic location:

Preferred name:

NM_000540.3(RYR1):c.7089C>T (p.Cys2363=)

HGVS:

NC_000019.10:g.38499696C>T
NG_008866.1:g.70997C>T
NM_000540.3:c.7089C>TMANE SELECT
NM_001042723.2:c.7089C>T
NP_000531.2:p.Cys2363=
NP_000531.2:p.Cys2363=
NP_001036188.1:p.Cys2363=
LRG_766t1:c.7089C>T
LRG_766:g.70997C>T
LRG_766p1:p.Cys2363=
NC_000019.9:g.38990336C>T
NM_000540.2:c.7089C>T
NP_000531.2:p.(=)

Links:

dbSNP: rs2228071

NCBI 1000 Genomes Browser:

rs2228071

Molecular consequence:

NM_000540.3:c.7089C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001042723.2:c.7089C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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Aloe lateritia voucher Brandham&Cutler19159 internal transcribed spacer 1, parti...
Aloe lateritia voucher Brandham&Cutler19159 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|749406139|gb|KJ557888.1|

Nucleotide
JGI_CABG8184.fwd NIH_XGC_tropSto1 Xenopus tropicalis cDNA clone IMAGE:7839607 5'...
JGI_CABG8184.fwd NIH_XGC_tropSto1 Xenopus tropicalis cDNA clone IMAGE:7839607 5', mRNA sequence
gi|71521504|gnl|dbEST|30384537|gb|D 14.1|

Nucleotide
Homo sapiens DNA repair protein RAD52 gamma isoform (RAD52) mRNA, alternatively ...
Homo sapiens DNA repair protein RAD52 gamma isoform (RAD52) mRNA, alternatively spliced, complete cds
gi|4581007|gb|AF125949.1|

Nucleotide
Related DataSets for GEO Profiles (Select 61703837) (1)
GEO DataSets
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Ovarian normal surface epithelia and ovarian cancer epithelial cells
Accession: GDS3592

GEO DataSets

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000111030	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (May 7, 2013)	germline	clinical testing	Citation Link,
SCV000194850	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Benign (Aug 15, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000304994	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Mar 29, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000518380	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Sep 28, 2015)	germline	clinical testing	Citation Link,
SCV000711707	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Jan 13, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	6	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

See all PubMed Citations (3)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000111030.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		6	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV000194850.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000304994.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV000518380.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000711707.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

p.Cys2363Cys in exon 44 of RYR1: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 5.7% (490/8598) o f European American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2228071).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		1	not provided	1	not provided

Last Updated: Sep 29, 2024

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