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Reference SNP (refSNP) Cluster Report: rs13306487                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:121/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G/T (FWD)
Allele Origin:A:germline
G:germline
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:A=0.0023/281 (ExAC)
A=0.0038/19 (1000 Genomes)
A=0.0002/2 (GO-ESP)
A=0.0022/271 (TOPMED)
HGVS Names
  • CM000679.2:g.47292422G>A
  • CM000679.2:g.47292422G>C
  • CM000679.2:g.47292422G>T
  • NC_000017.10:g.45369788G>A
  • NC_000017.10:g.45369788G>C
  • NC_000017.10:g.45369788G>T
  • NC_000017.11:g.47292422G>A
  • NC_000017.11:g.47292422G>C
  • NC_000017.11:g.47292422G>T
  • NG_008332.2:g.43581G>A
  • NG_008332.2:g.43581G>C
  • NG_008332.2:g.43581G>T
  • NM_000212.2:c.1544G>A
  • NM_000212.2:c.1544G>C
  • NM_000212.2:c.1544G>T
  • NP_000203.2:p.Arg515Gln
  • NP_000203.2:p.Arg515Leu
  • NP_000203.2:p.Arg515Pro
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss275518100 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13306487 during BLAST analysis for the current build.


NCBI
Assay ID
Handle|Submitter IDValidation
Status
ss to rs
Orientation
/Strand
Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date
Update
Date
Build
Added
Molecule
Type
Freq
Warning
Ancestral
Allele
Success
Rate
ss22887389IMCJ-GDT|IMCJ-ITGB3_4-AGfwd/TA/Ggcccttcccagcaggacgantgcagcccccngagggtcagcccgtctgcagccagcgggg03/22/0403/22/04121Genomicunknown
ss161059342ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP17-42724787-0_B_R_1588119235rev/BC/Tccccgctggctgcagacgggctgaccctccgggggctgcattcgtcctgctgggaagggc08/04/0910/05/09131Genomicunknown
ss2435481171000GENOMES|pilot_1_CHB+JPT_5433194_chr17_42724787fwd/A/Ggcccttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccagcgggg05/01/1005/01/10132Genomicunknown
ss275518100OMIM-CURATED-RECORDS|4734fwd/TA/Ggcccttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccagcgggg12/03/1012/03/10133Genomicunknown
ss342457101NHLBI-ESP|ESP2500-chr17-45369788fwd/TA/Ggcccttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccagcgggg03/25/1103/27/11134Genomicunknown
ss479202225ILLUMINA|HumanOmni1-Quad_v1-0_C_kgp14083607-0_B_R_1831811015fwd/TA/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag01/30/1208/28/15146Genomicunknown
ss4911258541000GENOMES|20110521_exome_633652_chr17_45369788fwd/TA/Ggcccttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccagcgggg02/10/1202/22/12137Genomicunknown
ss491524001EXOME_CHIP|nonsyn_240227_chr_17_45369788fwd/TA/Ggcccttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccagcgggg03/05/1203/06/12137Genomicunknown
ss533777431ILLUMINA|HumanOmni5-4v1_B_kgp14083607-0_T_F_1831811014fwd/TA/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag06/22/1208/29/15146Genomicunknown
ss661095467SSMP|17_45369788fwd/TA/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag12/14/1202/14/15138Genomicunknown
ss13587743621000GENOMES|PHASE3_V1_72311996fwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag08/16/1408/16/14142Genomicunknown
ss1584106928EVA_FINRISK|EVA_FINRISK_rs13306487fwd/TA/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag02/27/1502/27/15144Genomicunknown
ss1635708121EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_17_45369788_39910775fwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag03/04/1503/04/15144Genomicunknown
ss1678702154EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_17_45369788_39910775fwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag03/04/1503/04/15144Genomicunknown
ss1692833527EVA_EXAC|EVA_EXAC_8210300fwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag03/04/1503/04/15144Genomicunknown
ss1692833528EVA_EXAC|EVA_EXAC_8210301fwd/C/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag03/04/1503/04/15144Genomicunknown
ss1711464025EVA_MGP|EVA_XIMO_579785fwd/TA/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag03/09/1503/09/15144Genomicunknown
ss1959750751ILLUMINA|17:45369788-GA-0_B_R_2299475127fwd/TA/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag11/13/1511/13/15147Genomicunknown
ss2217066065HUMAN_LONGEVITY|HLI-17-47292422-G-A,Tfwd/A/G/Ttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag11/18/1611/18/16150Genomicunknown
ss2382209954TOPMED|17_45369788_G/Afwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag11/19/1611/19/16150Genomicunknown
ss2702110218GRF|rs13306487fwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag02/13/1702/13/17151Genomicunknown
ss2742803961GNOMAD|exomes_rs13306487fwd/A/C/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag05/17/1705/17/17151Genomicunknown
ss2749800769GNOMAD|coding_rs13306487fwd/A/G/Ttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag05/17/1705/17/17151Genomicunknown
ss2950241017GNOMAD|rs13306487fwd/A/G/Ttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag05/23/1705/23/17151Genomicunknown
ss2985732767AFFY|Axiom_Smokesc1_Affx-13947903fwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag05/24/1705/24/17151Genomicunknown
ss3015590080SWEGEN|NC_000017.10:g.45369788G>Afwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag05/30/1705/30/17151Genomicunknown
ss3021784529ILLUMINA|MEGA_Consortium_v2_15070954_A2_17:45369788-GA-0_B_R_2299475127fwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag06/28/1706/28/17151Genomicunknown
ss3263675963TOPMED|TOPMed_freeze_5?chr17:47,292,422-01fwd/A/Gtcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag10/01/1710/01/17151Genomicunknown
ss3263675964TOPMED|TOPMed_freeze_5?chr17:47,292,422-02fwd/G/Ttcccagcaggacgaatgcagcccccggagggtcagcccgtctgcagccag10/01/1710/01/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs13306487|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/C/G/T'|mol=Genomic|build=151
 TGTCCCCAGG AGAAGGAGAA GTCCTTTACC ATAAAGCCCG TGGGCTTCAA GGACAGCCTG
 ATCGTCCAGG TCACCTTTGA TTGTGACTGT GCCTGCCAGG CCCAAGCTGA ACCTAATAGC
 CATCGCTGCA ACAATGGCAA TGGGACCTTT GAGTGTGGGG TATGCCGTTG TGGGCCTGGC
 TGGCTGGGAT CCCAGTGTGA GTGCTCAGAG GAGGACTATC GCCCTTCCCA GCAGGACGAA
 TGCAGCCCCC
 N
 GGAGGGTCAG CCCGTCTGCA GCCAGCGGGG CGAGTGCCTC TGTGGTCAAT GTGTCTGCCA
 CAGCAGTGAC TTTGGCAAGA TCACGGGCAA GTACTGCGAG TGTGACGACT TCTCCTGTGT
 CCGCTACAAG GGGGAGATGT GCTCAGGTGA GGAGAACTGC AGGGCCCCCT GTCCTGGAAC
 CCACACCCCC TCATATACCT GCAACCACTG GAAACATAGG TGAAGGCCTG AGATGGGTCT
 TTGCAGGCAG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000017
dbSNP Blast Analysis
UniGene Cluster ID
218040
3D structure mapping
NP_000203  
OMIM
173470.0009

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
C
G
ss1358774362EAS 1008AF 0.01490000 0.98509997
EUR 1006AF 0.00300000 0.99699998
AFR 1322AF 0.00080000 0.99919999
AMR 694AF 1.00000000
SAS 978AF 1.00000000
ss1692833527ExAc_Aggregated_Populations121409AF 0.00232273 0.99767727
ss1692833528ExAc_Aggregated_Populations121128AF 0.000008260.99999171
ss22887389ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss243548117pilot_1_CHB+JPT_low_coverage_panel 120AF 0.05000000 0.94999999
ss342457101ESP_Cohort_Populations 4552GF 0.000439370.999560651.000000000.00021968 0.99978030

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.005+/-0.0480000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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