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NM_014159.7(SETD2):c.5900G>A (p.Gly1967Asp) AND not specified

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Nov 23, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000122016.7

Allele description [Variation Report for NM_014159.7(SETD2):c.5900G>A (p.Gly1967Asp)]

NM_014159.7(SETD2):c.5900G>A (p.Gly1967Asp)

Gene:
SETD2:SET domain containing 2, histone lysine methyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_014159.7(SETD2):c.5900G>A (p.Gly1967Asp)
HGVS:
  • NC_000003.12:g.47083880C>T
  • NG_032091.1:g.85098G>A
  • NM_001349370.3:c.5768G>A
  • NM_014159.7:c.5900G>AMANE SELECT
  • NP_001336299.1:p.Gly1923Asp
  • NP_054878.5:p.Gly1967Asp
  • NP_054878.5:p.Gly1967Asp
  • LRG_775t1:c.5900G>A
  • LRG_775:g.85098G>A
  • LRG_775p1:p.Gly1967Asp
  • NC_000003.11:g.47125370C>T
  • NM_014159.6:c.5900G>A
  • NR_146158.3:n.6089G>A
Protein change:
G1923D
Links:
dbSNP: rs143991928
NCBI 1000 Genomes Browser:
rs143991928
Molecular consequence:
  • NM_001349370.3:c.5768G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014159.7:c.5900G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_146158.3:n.6089G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000086227ITMI
no classification provided
not providedgermlinereference population

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

SCV000597005Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Nov 23, 2016)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
Africangermlineunknownnot providednot providednot provided43not providedreference population
African_Europeangermlineunknownnot providednot providednot provided46not providedreference population
Central_Asiangermlineunknownnot providednot providednot provided50not providedreference population
East_Asiangermlineunknownnot providednot providednot provided62not providedreference population
Europeangermlineunknownnot providednot providednot provided331not providedreference population
Hispanicgermlineunknownnot providednot providednot provided118not providedreference population
Whole_cohortgermlineunknownnot providednot providednot provided681not providedreference population

Citations

PubMed

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]
PMID:
24728327
PMCID:
PMC3984285

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 ITMI, SCV000086227.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Africannot providednot providednot providedreference population PubMed (1)
2African_Europeannot providednot providednot providedreference population PubMed (1)
3Central_Asiannot providednot providednot providedreference population PubMed (1)
4East_Asiannot providednot providednot providedreference population PubMed (1)
5Europeannot providednot providednot providedreference population PubMed (1)
6Hispanicnot providednot providednot providedreference population PubMed (1)
7Whole_cohortnot providednot providednot providedreference population PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown43not provideddiscoverynot provided0not providednot provided
2germlineunknown46not provideddiscoverynot provided0.0109not providednot provided
3germlineunknown50not provideddiscoverynot provided0not providednot provided
4germlineunknown62not provideddiscoverynot provided0not providednot provided
5germlineunknown331not provideddiscoverynot provided0not providednot provided
6germlineunknown118not provideddiscoverynot provided0not providednot provided
7germlineunknown681not provideddiscoverynot provided0.0007not providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000597005.1

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

Last Updated: Jul 7, 2024