NM_003002.3(SDHD):c.204C>T (p.Ser68=) AND not specified

Clinical significance:Conflicting interpretations of pathogenicity, Benign(2);Likely benign(1) (Last evaluated: Dec 21, 2012)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000037727.5

Allele description [Variation Report for NM_003002.3(SDHD):c.204C>T (p.Ser68=)]

NM_003002.3(SDHD):c.204C>T (p.Ser68=)

Gene:
SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.1
Genomic location:
Preferred name:
NM_003002.3(SDHD):c.204C>T (p.Ser68=)
HGVS:
  • NC_000011.10:g.112088901C>T
  • NG_012337.3:g.7055C>T
  • NM_001276503.1:c.169+928C>T
  • NM_003002.3:c.204C>T
  • NP_002993.1:p.Ser68=
  • NC_000011.9:g.111959625C>T
  • NM_003002.2:c.204C>T
  • NR_077060.1:n.288C>T
  • c.204C>T
  • p.S68S
  • p.Ser68Ser
Links:
dbSNP: 9919552
GMAF:
0.1134(T), 9919552
NCBI 1000 Genomes Browser:
rs9919552
Allele Frequency:
NaN, GO-ESP
Molecular consequence:
  • NM_001276503.1:c.169+928C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_077060.1:n.288C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_003002.3:c.204C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
5

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000061389Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(Dec 21, 2012)
germlineclinical testing

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

SCV000194885Genetic Services Laboratory, University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000309338PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed

SCV000194885

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot provided55not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

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

Details of each submission

From Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine, SCV000061389.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (1)

Description

This variant is classified as benign because it does not change the amino acid and is frequent in the general population (rs9919552, MAF >1%). Noted as 2.8-4.4% in TCA gene mutation database.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided5not provided5not provided

From Genetic Services Laboratory, University of Chicago, SCV000194885.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From PreventionGenetics, SCV000309338.1

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

Last Updated: Jun 20, 2017