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rs6939340

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(A;A) 0 normal
(A;G) 1.42x possible increased risk for neuroblastoma
(G;G) 2x increased risk for neuroblastoma
ReferenceGRCh38 38.1/141
Chromosome6
Position22139775
GeneLINC00340, P2RX7
is asnp
is mentioned by
dbSNPrs6939340
ebirs6939340
HLIrs6939340
Exacrs6939340
Varsomers6939340
Maprs6939340
PheGenIrs6939340
hapmaprs6939340
1000 genomesrs6939340
hgdprs6939340
ensemblrs6939340
gopubmedrs6939340
geneviewrs6939340
scholarrs6939340
googlers6939340
pharmgkbrs6939340
gwascentralrs6939340
openSNPrs6939340
23andMers6939340
23andMe allrs6939340
SNP Nexus

SNPshotrs6939340
SNPdbers6939340
MSV3drs6939340
GWAS Ctlgrs6939340
GMAF0.3471
Max Magnitude0
? (A;A) (A;G) (G;G) 28
SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs6939340(G;G) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.97, CI: 1.58 to 2.45, p=9.3 x 10-15). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival.[PMID 18463370OA-icon.png]

Presumably driven primarily by the at-risk homozygotes, the rs6939340(G) allele was considered to be a risk factor, however, there was insufficient data to conclude whether rs6939340(A;G) heterozygotes were actually at any increased risk compared to rs6939340(A;A) "wild-type" homozygotes.[PMID 18463370OA-icon.png]

Note that this is an excellent example for putting SNP-associated risks in a relative context of Lifetime Risk. The annual mortality rate for neuroblastoma for everyone combined is 10 per 1 million children in the 0- to 4-year-old age group. Assuming the ~20% of children with the most "at-risk" genotype identified to date, i.e. rs6939340(G;G) homozygotes, have double the risk of the other genotypes, which means their mortality risk has only gone up to ~17 per million, versus the risk for the 80% of individuals with other genotypes going down to ~9 per million. Even if these studies are successfully replicated, odds of 17 out of a million are very very small, so these studies are not useful in predicting disease, even if they may ultimately have benefit in the management of individuals diagnosed with disease.

GWAS
SNP rs6939340
PubMedID [PMID 18463370OA-icon.png]
Condition Neuroblastoma
Gene FLJ22536, FLJ44180
Risk Allele G
pValue 9.00E-015
OR 1.37
95% CI 1.27-1.49


OMIM256700
DescNEUROBLASTOMA
Variant
Relatedalso



OMIM613015
Desc
Variant
Relatedalso
[PMID 19412175OA-icon.png] Common variations in BARD1 influence susceptibility to high-risk neuroblastoma.


GET Evidence
rs6939340
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.650794
summary