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NM_000305.3(PON2):c.-5G>A AND not provided

Germline classification:
Benign (1 submission)
Last evaluated:
Nov 21, 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:
RCV000588428.1

Allele description [Variation Report for NM_000305.3(PON2):c.-5G>A]

NM_000305.3(PON2):c.-5G>A

Gene:
PON2:paraoxonase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.3
Genomic location:
Preferred name:
NM_000305.3(PON2):c.-5G>A
HGVS:
  • NC_000007.14:g.95434956C>T
  • NG_008725.1:g.5117G>A
  • NM_000305.3:c.-5G>AMANE SELECT
  • NM_001018161.2:c.-5G>A
  • NC_000007.13:g.95064268C>T
  • NM_000305.2:c.-5G>A
Links:
dbSNP: rs17876183
NCBI 1000 Genomes Browser:
rs17876183
Molecular consequence:
  • NM_000305.3:c.-5G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001018161.2:c.-5G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000696506Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Nov 21, 2016) 		germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696506.1

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

Description

Variant summary: The PON2 c.-5G>A variant involves the alteration of a non-conserved nucleotide in 5-prime untranslated region. This variant was found in 99/11484 control chromosomes (including 2 homozygotes), predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0143312 (45/3140). This frequency is about 717 times the estimated maximal expected allele frequency of a pathogenic PON2 variant (0.00002), suggesting this is very likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. The variant has been suggested to modestly increase risk for systemic lupus erythematosus (OR: 4.63 95% CI 1.37-15.59, P= 0.013) (Dasgupta_2011); however gene-phenotype link has not been ascertained thus needing further confirmation of the association. The variant has not been seen in patients with cardiac phenotype, to our knowledge. One internal sample screened for cardiac disease also carries LDLR p.E228X, supporting for a benign outcome. Taken together, this variant is classified as Benign.

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

Last Updated: May 19, 2024