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NM_014159.7(SETD2):c.19C>T (p.Gln7Ter) AND SETD2-related disorder

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jan 19, 2024
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:
RCV004533296.1

Allele description [Variation Report for NM_014159.7(SETD2):c.19C>T (p.Gln7Ter)]

NM_014159.7(SETD2):c.19C>T (p.Gln7Ter)

Genes:
LOC129936665:ATAC-STARR-seq lymphoblastoid silent region 14306 [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.19C>T (p.Gln7Ter)
HGVS:
  • NC_000003.12:g.47163906G>A
  • NG_032091.1:g.5072C>T
  • NM_001349370.3:c.-98C>T
  • NM_014159.7:c.19C>TMANE SELECT
  • NP_054878.5:p.Gln7Ter
  • NP_054878.5:p.Gln7Ter
  • LRG_775t1:c.19C>T
  • LRG_775:g.5072C>T
  • LRG_775p1:p.Gln7Ter
  • NC_000003.11:g.47205396G>A
  • NM_014159.6:c.19C>T
  • NR_146158.3:n.208C>T
Protein change:
Q7*
Links:
dbSNP: rs541943893
NCBI 1000 Genomes Browser:
rs541943893
Molecular consequence:
  • NM_001349370.3:c.-98C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_146158.3:n.208C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_014159.7:c.19C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
SETD2-related disorder
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004719680PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely benign
(Jan 19, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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 PreventionGenetics, part of Exact Sciences, SCV004719680.1

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

Description

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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

Last Updated: Sep 29, 2024