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NM_014159.7(SETD2):c.1414C>T (p.Arg472Cys) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 14, 2023
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:
RCV003362914.2

Allele description [Variation Report for NM_014159.7(SETD2):c.1414C>T (p.Arg472Cys)]

NM_014159.7(SETD2):c.1414C>T (p.Arg472Cys)

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.1414C>T (p.Arg472Cys)
HGVS:
  • NC_000003.12:g.47123222G>A
  • NG_032091.1:g.45756C>T
  • NM_001349370.3:c.1282C>T
  • NM_014159.7:c.1414C>TMANE SELECT
  • NP_001336299.1:p.Arg428Cys
  • NP_054878.5:p.Arg472Cys
  • NP_054878.5:p.Arg472Cys
  • LRG_775t1:c.1414C>T
  • LRG_775:g.45756C>T
  • LRG_775p1:p.Arg472Cys
  • NC_000003.11:g.47164712G>A
  • NM_014159.6:c.1414C>T
  • NR_146158.3:n.1603C>T
Protein change:
R428C
Links:
dbSNP: rs771203643
NCBI 1000 Genomes Browser:
rs771203643
Molecular consequence:
  • NM_001349370.3:c.1282C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014159.7:c.1414C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_146158.3:n.1603C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004064281Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Likely benign
(Aug 14, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV004064281.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: May 1, 2024